From 17ac41ee4d62e8d7489b7c04d877663f844934ff Mon Sep 17 00:00:00 2001 From: John-F-Wagstaff Date: Wed, 14 Jan 2026 15:59:47 +0000 Subject: [PATCH 1/2] Non list based, poly a requiring transcripts, fix Upgrade the initial poly a requiring transcripts fix by switching to methods that work without requiring an external, update requiring, list of known bad cases, to work. --- VariantValidator/modules/utils.py | 14 ++++++++------ VariantValidator/modules/vvMixinInit.py | 16 ++++------------ 2 files changed, 12 insertions(+), 18 deletions(-) diff --git a/VariantValidator/modules/utils.py b/VariantValidator/modules/utils.py index cd12d324..928c60d5 100644 --- a/VariantValidator/modules/utils.py +++ b/VariantValidator/modules/utils.py @@ -485,7 +485,7 @@ def pro_delins_info(prot_ref_seq, prot_var_seq, in_frame=False): return info -def translate(ed_seq, cds_start, modified_aa=None, tolerate_no_stop_cds=False, polyadenylate=False): +def translate(ed_seq, cds_start, modified_aa=None, tolerate_no_stop_cds=False): """ Translate c. reference sequences, including those that have been modified must have the CDS in the specified position @@ -512,10 +512,6 @@ def translate(ed_seq, cds_start, modified_aa=None, tolerate_no_stop_cds=False, p use_dict = PROT_TRANSLATION_DICT stops = ['TAA', 'TAG', 'TGA'] - # Add Polyadenylation stop codon completing bases to relevant transcripts - if polyadenylate is True: - coding_sequence = f"{coding_sequence}A" - # Translate if len(coding_sequence) % 3: last_codon_end = int(len(coding_sequence)/3) * 3 @@ -529,7 +525,13 @@ def translate(ed_seq, cds_start, modified_aa=None, tolerate_no_stop_cds=False, p break if translation[-1] != '*': if not tolerate_no_stop_cds: - raise IndexError('No stop CDS') + # Add Polyadenylation stop codon completing bases to relevant + # transcripts + spare_end = len(coding_sequence) % 3 + if spare_end and coding_sequence[-spare_end:] in ['T','TA']: + translation.append('*') + else: + raise IndexError('No stop CDS') translation.append('X') return "".join(translation) diff --git a/VariantValidator/modules/vvMixinInit.py b/VariantValidator/modules/vvMixinInit.py index 4eebd622..47a2f838 100644 --- a/VariantValidator/modules/vvMixinInit.py +++ b/VariantValidator/modules/vvMixinInit.py @@ -15,7 +15,6 @@ import vvhgvs.normalizer from vvhgvs.location import AAPosition, Interval from vvhgvs.edit import AARefAlt, AAExt, Dup -from vvhgvs.utils import unusual_transcripts from Bio.Seq import Seq import re @@ -460,23 +459,16 @@ def _remake_unc(prot,nucleotide_not_equal=False): else: modified_aa = None - # Add Polyadenylation stop codon completing bases to relevant transcripts - require_A = unusual_transcripts.polyadnylate() - if hgvs_transcript.ac in require_A: - polyadenylate = True - else: - polyadenylate = False - # Translate the reference and variant proteins try: - prot_ref_seq = utils.translate(ref_seq, cds_start, modified_aa, polyadenylate=polyadenylate) + prot_ref_seq = utils.translate(ref_seq, cds_start, modified_aa) except IndexError: import traceback traceback.print_exc() hgvs_transcript_to_hgvs_protein['error'] = \ 'ProteinTranslationError: Cannot generate a protein without an identifiable in-' +\ 'frame Termination codon in the reference mRNA sequence, this transcript may be ' +\ - 'subject to non-sense mediated decay' + 'subject to non-stop mediated decay' hgvs_transcript_to_hgvs_protein['hgvs_protein'] = _tot_unc(associated_protein_accession) return hgvs_transcript_to_hgvs_protein except KeyError: @@ -491,12 +483,12 @@ def _remake_unc(prot,nucleotide_not_equal=False): try: - prot_var_seq = utils.translate(var_seq, cds_start, modified_aa, polyadenylate=polyadenylate) + prot_var_seq = utils.translate(var_seq, cds_start, modified_aa) except IndexError: hgvs_transcript_to_hgvs_protein['error'] = \ 'ProteinTranslationError: Cannot generate a protein without an identifiable in-' +\ 'frame Termination codon in the variant mRNA sequence, this transcript may be ' +\ - 'subject to nonstop decay' + 'subject to non-stop decay' hgvs_protein = _tot_unc(associated_protein_accession) hgvs_transcript_to_hgvs_protein['hgvs_protein'] = hgvs_protein return hgvs_transcript_to_hgvs_protein From 8252127de6f1c6f96c612d96a3cf8c9806972c2e Mon Sep 17 00:00:00 2001 From: John-F-Wagstaff Date: Wed, 14 Jan 2026 16:12:29 +0000 Subject: [PATCH 2/2] Git ignore and tidy up batch input/output --- batch/.gitignore | 4 +++ batch/input.txt | 35 ----------------------- batch/output.txt | 72 ------------------------------------------------ 3 files changed, 4 insertions(+), 107 deletions(-) create mode 100644 batch/.gitignore delete mode 100644 batch/input.txt delete mode 100644 batch/output.txt diff --git a/batch/.gitignore b/batch/.gitignore new file mode 100644 index 00000000..aad362b0 --- /dev/null +++ b/batch/.gitignore @@ -0,0 +1,4 @@ +# Ignore all files and subdirectories +* +# But make an exception for just this .gitignore file +!.gitignore diff --git a/batch/input.txt b/batch/input.txt deleted file mode 100644 index 0eaf8205..00000000 --- a/batch/input.txt +++ /dev/null @@ -1,35 +0,0 @@ -2:g.46706765C>T -2:g.46706796G>T -2:g.46706863A>C -2:g.46706866A>C -2:g.46706872G>A -2:g.46707595G>C -2:g.46707674C>T -2:g.46707698A>G -2:g.46707701T>C -2:g.46707709A>G -2:g.46707806G>A -2:g.46707827T>C -2:g.46707839T>C -2:g.46707851G>A -2:g.46707864G>A -2:g.46707878_46707879insGCAGCGGGAGCG -2:g.46707883_46707884insGG -2:g.46707884A>G -2:g.46707885A>C -2:g.46707885A>G -2:g.46707886G>A -2:g.46707887A>C -2:g.46707888delG -2:g.46707888G>A -2:g.46707888_46707889insGTGGTGATGGA -2:g.46707888_46707889insGTGGTGATGGAGCA -2:g.46707888_46707889insGTGGTGATGGAGCAGCT -2:g.46707891G>A -2:g.46707894G>A -2:g.46707895C>G -2:g.46707897C>A -2:g.46711338G>A -2:g.46711378_46711379delCA -2:g.46711403C>A -2:g.46711500G>A diff --git a/batch/output.txt b/batch/output.txt deleted file mode 100644 index 75968ab7..00000000 --- a/batch/output.txt +++ /dev/null @@ -1,72 +0,0 @@ -# Metadata: variantvalidator_version: 2.2.1.dev962+gf14a63044, variantvalidator_hgvs_version: 2.2.1.dev16+ge2404ca49, vvta_version: vvta_2025_02, vvseqrepo_db: VV_SR_2025_02/master, vvdb_version: vvdb_2025_3 -Input Warnings Select transcript HGVS_transcript HGVS_intronic_chr_context HGVS_intronic_rsg_context HGVS_RefSeqGene HGVS_LRG HGVS_LRG_transcript HGVS_Predicted_Protein HGVS_Genomic_GRCh37 GRCh37_CHR GRCh37_POS GRCh37_ID GRCh37_REF GRCh37_ALT HGVS_Genomic_GRCh38 GRCh38_CHR GRCh38_POS GRCh38_ID GRCh38_REF GRCh38_ALT Gene_Symbol HGNC_Gene_ID Transcript_description Alt_genomic_loci -2:g.46706765C>T None False NM_001145051.2:c.41C>T None None None None None NP_001138523.1:p.(Ala14Val) NC_000002.11:g.46706765C>T 2 46706765 . C T NC_000002.12:g.46479626C>T 2 46479626 . C T TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46706765C>T None MANE NM_001424184.1:c.41C>T None None None None None NP_001411113.1:p.(Ala14Val) NC_000002.11:g.46706765C>T 2 46706765 . C T NC_000002.12:g.46479626C>T 2 46479626 . C T TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46706796G>T None False NM_001145051.2:c.72G>T None None None None None NP_001138523.1:p.(Met24Ile) NC_000002.11:g.46706796G>T 2 46706796 . G T NC_000002.12:g.46479657G>T 2 46479657 . G T TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46706796G>T None MANE NM_001424184.1:c.72G>T None None None None None NP_001411113.1:p.(Met24Ile) NC_000002.11:g.46706796G>T 2 46706796 . G T NC_000002.12:g.46479657G>T 2 46479657 . G T TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46706863A>C None False NM_001145051.2:c.117+22A>C NC_000002.11(NM_001145051.2):c.117+22A>C None None None None NP_001138523.1:p.? NC_000002.11:g.46706863A>C 2 46706863 . A C NC_000002.12:g.46479724A>C 2 46479724 . A C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46706863A>C None MANE NM_001424184.1:c.117+22A>C NC_000002.11(NM_001424184.1):c.117+22A>C None None None None NP_001411113.1:p.? NC_000002.11:g.46706863A>C 2 46706863 . A C NC_000002.12:g.46479724A>C 2 46479724 . A C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46706866A>C None False NM_001145051.2:c.117+25A>C NC_000002.11(NM_001145051.2):c.117+25A>C None None None None NP_001138523.1:p.? NC_000002.11:g.46706866A>C 2 46706866 . A C NC_000002.12:g.46479727A>C 2 46479727 . A C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46706866A>C None MANE NM_001424184.1:c.117+25A>C NC_000002.11(NM_001424184.1):c.117+25A>C None None None None NP_001411113.1:p.? NC_000002.11:g.46706866A>C 2 46706866 . A C NC_000002.12:g.46479727A>C 2 46479727 . A C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46706872G>A None False NM_001145051.2:c.117+31G>A NC_000002.11(NM_001145051.2):c.117+31G>A None None None None NP_001138523.1:p.? NC_000002.11:g.46706872G>A 2 46706872 . G A NC_000002.12:g.46479733G>A 2 46479733 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46706872G>A None MANE NM_001424184.1:c.117+31G>A NC_000002.11(NM_001424184.1):c.117+31G>A None None None None NP_001411113.1:p.? NC_000002.11:g.46706872G>A 2 46706872 . G A NC_000002.12:g.46479733G>A 2 46479733 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707595G>C None False NM_001145051.2:c.169G>C None None None None None NP_001138523.1:p.(Glu57Gln) NC_000002.11:g.46707595G>C 2 46707595 . G C NC_000002.12:g.46480456G>C 2 46480456 . G C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707595G>C None MANE NM_001424184.1:c.169G>C None None None None None NP_001411113.1:p.(Glu57Gln) NC_000002.11:g.46707595G>C 2 46707595 . G C NC_000002.12:g.46480456G>C 2 46480456 . G C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707674C>T None False NM_001145051.2:c.248C>T None None None None None NP_001138523.1:p.(Ala83Val) NC_000002.11:g.46707674C>T 2 46707674 . C T NC_000002.12:g.46480535C>T 2 46480535 . C T TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707674C>T None MANE NM_001424184.1:c.248C>T None None None None None NP_001411113.1:p.(Ala83Val) NC_000002.11:g.46707674C>T 2 46707674 . C T NC_000002.12:g.46480535C>T 2 46480535 . C T TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707698A>G None False NM_001145051.2:c.272A>G None None None None None NP_001138523.1:p.(Glu91Gly) NC_000002.11:g.46707698A>G 2 46707698 . A G NC_000002.12:g.46480559A>G 2 46480559 . A G TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707698A>G None MANE NM_001424184.1:c.272A>G None None None None None NP_001411113.1:p.(Glu91Gly) NC_000002.11:g.46707698A>G 2 46707698 . A G NC_000002.12:g.46480559A>G 2 46480559 . A G TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707701T>C None False NM_001145051.2:c.275T>C None None None None None NP_001138523.1:p.(Leu92Pro) NC_000002.11:g.46707701T>C 2 46707701 . T C NC_000002.12:g.46480562T>C 2 46480562 . T C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707701T>C None MANE NM_001424184.1:c.275T>C None None None None None NP_001411113.1:p.(Leu92Pro) NC_000002.11:g.46707701T>C 2 46707701 . T C NC_000002.12:g.46480562T>C 2 46480562 . T C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707709A>G None False NM_001145051.2:c.283A>G None None None None None NP_001138523.1:p.(Thr95Ala) NC_000002.11:g.46707709A>G 2 46707709 . A G NC_000002.12:g.46480570A>G 2 46480570 . A G TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707709A>G None MANE NM_001424184.1:c.283A>G None None None None None NP_001411113.1:p.(Thr95Ala) NC_000002.11:g.46707709A>G 2 46707709 . A G NC_000002.12:g.46480570A>G 2 46480570 . A G TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707806G>A None False NM_001145051.2:c.380G>A None None None None None NP_001138523.1:p.(Arg127Gln) NC_000002.11:g.46707806G>A 2 46707806 . G A NC_000002.12:g.46480667G>A 2 46480667 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707806G>A None MANE NM_001424184.1:c.380G>A None None None None None NP_001411113.1:p.(Arg127Gln) NC_000002.11:g.46707806G>A 2 46707806 . G A NC_000002.12:g.46480667G>A 2 46480667 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707827T>C None False NM_001145051.2:c.401T>C None None None None None NP_001138523.1:p.(Val134Ala) NC_000002.11:g.46707827T>C 2 46707827 . T C NC_000002.12:g.46480688T>C 2 46480688 . T C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707827T>C None MANE NM_001424184.1:c.401T>C None None None None None NP_001411113.1:p.(Val134Ala) NC_000002.11:g.46707827T>C 2 46707827 . T C NC_000002.12:g.46480688T>C 2 46480688 . T C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707839T>C None False NM_001145051.2:c.413T>C None None None None None NP_001138523.1:p.(Leu138Pro) NC_000002.11:g.46707839T>C 2 46707839 . T C NC_000002.12:g.46480700T>C 2 46480700 . T C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707839T>C None MANE NM_001424184.1:c.413T>C None None None None None NP_001411113.1:p.(Leu138Pro) NC_000002.11:g.46707839T>C 2 46707839 . T C NC_000002.12:g.46480700T>C 2 46480700 . T C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707851G>A None False NM_001145051.2:c.425G>A None None None None None NP_001138523.1:p.(Arg142Gln) NC_000002.11:g.46707851G>A 2 46707851 . G A NC_000002.12:g.46480712G>A 2 46480712 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707851G>A None MANE NM_001424184.1:c.425G>A None None None None None NP_001411113.1:p.(Arg142Gln) NC_000002.11:g.46707851G>A 2 46707851 . G A NC_000002.12:g.46480712G>A 2 46480712 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707864G>A None False NM_001145051.2:c.438G>A None None None None None NP_001138523.1:p.(Val146=) NC_000002.11:g.46707864G>A 2 46707864 . G A NC_000002.12:g.46480725G>A 2 46480725 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707864G>A None MANE NM_001424184.1:c.438G>A None None None None None NP_001411113.1:p.(Ter220XaaextTer?) NC_000002.11:g.46707864G>A 2 46707864 . G A NC_000002.12:g.46480725G>A 2 46480725 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707878_46707879insGCAGCGGGAGCG None False NM_001145051.2:c.457_458insGGGAGCGGCAGC None None None None None NP_001138523.1:p.(Gln152_Gln153insArgGluArgGln) NC_000002.11:g.46707883_46707884insGGGAGCGGCAGC 2 46707878 . T TGCAGCGGGAGCG NC_000002.12:g.46480744_46480745insGGGAGCGGCAGC 2 46480739 . T TGCAGCGGGAGCG TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707878_46707879insGCAGCGGGAGCG None MANE NM_001424184.1:c.457_458insGGGAGCGGCAGC None None None None None NP_001411113.1:p.(Gln153_Ter220delinsArgGluArgGlnGlnGluAlaAlaProArgLeuPheSerGlyGlyLeuGlnAsnPheLeuLeuProGlnAsnGlnPheAlaMetPheLeuTyrCysPheIlePheIleHisIleIleTyrValThrLysGluMetValPhePheLeuPheAlaLysHisTyrLeuPheCysIleAlaAlaIleLeuLeuCysLeuIleLysThrPheTrpSerXaa) NC_000002.11:g.46707883_46707884insGGGAGCGGCAGC 2 46707878 . T TGCAGCGGGAGCG NC_000002.12:g.46480744_46480745insGGGAGCGGCAGC 2 46480739 . T TGCAGCGGGAGCG TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707883_46707884insGG None False NM_001145051.2:c.457_458insGG None None None None None NP_001138523.1:p.(Gln153ArgfsTer62) NC_000002.11:g.46707883_46707884insGG 2 46707883 . C CGG NC_000002.12:g.46480744_46480745insGG 2 46480744 . C CGG TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707883_46707884insGG None MANE NM_001424184.1:c.457_458insGG None None None None None NP_001411113.1:p.(Gln153ArgfsTer62) NC_000002.11:g.46707883_46707884insGG 2 46707883 . C CGG NC_000002.12:g.46480744_46480745insGG 2 46480744 . C CGG TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707884A>G None False NM_001145051.2:c.458A>G None None None None None NP_001138523.1:p.(Gln153Arg) NC_000002.11:g.46707884A>G 2 46707884 . A G NC_000002.12:g.46480745A>G 2 46480745 . A G TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707884A>G None MANE NM_001424184.1:c.458A>G None None None None None NP_001411113.1:p.(Gln153Arg) NC_000002.11:g.46707884A>G 2 46707884 . A G NC_000002.12:g.46480745A>G 2 46480745 . A G TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707885A>C None False NM_001145051.2:c.459A>C None None None None None NP_001138523.1:p.(Gln153His) NC_000002.11:g.46707885A>C 2 46707885 . A C NC_000002.12:g.46480746A>C 2 46480746 . A C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707885A>C None MANE NM_001424184.1:c.459A>C None None None None None NP_001411113.1:p.(Gln153His) NC_000002.11:g.46707885A>C 2 46707885 . A C NC_000002.12:g.46480746A>C 2 46480746 . A C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707885A>G None False NM_001145051.2:c.459A>G None None None None None NP_001138523.1:p.(Gln153=) NC_000002.11:g.46707885A>G 2 46707885 . A G NC_000002.12:g.46480746A>G 2 46480746 . A G TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707885A>G None MANE NM_001424184.1:c.459A>G None None None None None NP_001411113.1:p.(Ter220XaaextTer?) NC_000002.11:g.46707885A>G 2 46707885 . A G NC_000002.12:g.46480746A>G 2 46480746 . A G TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707886G>A None False NM_001145051.2:c.460G>A None None None None None NP_001138523.1:p.(Glu154Lys) NC_000002.11:g.46707886G>A 2 46707886 . G A NC_000002.12:g.46480747G>A 2 46480747 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707886G>A None MANE NM_001424184.1:c.460G>A None None None None None NP_001411113.1:p.(Glu154Lys) NC_000002.11:g.46707886G>A 2 46707886 . G A NC_000002.12:g.46480747G>A 2 46480747 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707887A>C None False NM_001145051.2:c.461A>C None None None None None NP_001138523.1:p.(Glu154Ala) NC_000002.11:g.46707887A>C 2 46707887 . A C NC_000002.12:g.46480748A>C 2 46480748 . A C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707887A>C None MANE NM_001424184.1:c.461A>C None None None None None NP_001411113.1:p.(Glu154Ala) NC_000002.11:g.46707887A>C 2 46707887 . A C NC_000002.12:g.46480748A>C 2 46480748 . A C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707888delG VariantSyntaxError: Removing redundant reference bases from variant description False NM_001145051.2:c.463del None None None None None NP_001138523.1:p.(Ala155ArgfsTer59) NC_000002.11:g.46707889del 2 46707887 . AG A NC_000002.12:g.46480750del 2 46480748 . AG A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707888delG VariantSyntaxError: Removing redundant reference bases from variant description MANE NM_001424184.1:c.463del None None None None None NP_001411113.1:p.(Ala155ArgfsTer59) NC_000002.11:g.46707889del 2 46707887 . AG A NC_000002.12:g.46480750del 2 46480748 . AG A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707888G>A None False NM_001145051.2:c.462G>A None None None None None NP_001138523.1:p.(Glu154=) NC_000002.11:g.46707888G>A 2 46707888 . G A NC_000002.12:g.46480749G>A 2 46480749 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707888G>A None MANE NM_001424184.1:c.462G>A None None None None None NP_001411113.1:p.(Ter220XaaextTer?) NC_000002.11:g.46707888G>A 2 46707888 . G A NC_000002.12:g.46480749G>A 2 46480749 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707888_46707889insGTGGTGATGGA None False NM_001145051.2:c.463_464insTGGTGATGGAG None None None None None NP_001138523.1:p.(Ala155ValfsTer63) NC_000002.11:g.46707889_46707890insTGGTGATGGAG 2 46707888 . G GGTGGTGATGGA NC_000002.12:g.46480750_46480751insTGGTGATGGAG 2 46480749 . G GGTGGTGATGGA TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707888_46707889insGTGGTGATGGA None MANE NM_001424184.1:c.463_464insTGGTGATGGAG None None None None None NP_001411113.1:p.(Ala155ValfsTer63) NC_000002.11:g.46707889_46707890insTGGTGATGGAG 2 46707888 . G GGTGGTGATGGA NC_000002.12:g.46480750_46480751insTGGTGATGGAG 2 46480749 . G GGTGGTGATGGA TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707888_46707889insGTGGTGATGGAGCA None False NM_001145051.2:c.463_464insTGGTGATGGAGCAG None None None None None NP_001138523.1:p.(Ala155ValfsTer64) NC_000002.11:g.46707889_46707890insTGGTGATGGAGCAG 2 46707888 . G GGTGGTGATGGAGCA NC_000002.12:g.46480750_46480751insTGGTGATGGAGCAG 2 46480749 . G GGTGGTGATGGAGCA TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707888_46707889insGTGGTGATGGAGCA None MANE NM_001424184.1:c.463_464insTGGTGATGGAGCAG None None None None None NP_001411113.1:p.(Ala155ValfsTer64) NC_000002.11:g.46707889_46707890insTGGTGATGGAGCAG 2 46707888 . G GGTGGTGATGGAGCA NC_000002.12:g.46480750_46480751insTGGTGATGGAGCAG 2 46480749 . G GGTGGTGATGGAGCA TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707888_46707889insGTGGTGATGGAGCAGCT None False NM_001145051.2:c.463_464insTGGTGATGGAGCAGCTG None None None None None NP_001138523.1:p.(Ala155ValfsTer65) NC_000002.11:g.46707889_46707890insTGGTGATGGAGCAGCTG 2 46707888 . G GGTGGTGATGGAGCAGCT NC_000002.12:g.46480750_46480751insTGGTGATGGAGCAGCTG 2 46480749 . G GGTGGTGATGGAGCAGCT TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707888_46707889insGTGGTGATGGAGCAGCT None MANE NM_001424184.1:c.463_464insTGGTGATGGAGCAGCTG None None None None None NP_001411113.1:p.(Ala155ValfsTer65) NC_000002.11:g.46707889_46707890insTGGTGATGGAGCAGCTG 2 46707888 . G GGTGGTGATGGAGCAGCT NC_000002.12:g.46480750_46480751insTGGTGATGGAGCAGCTG 2 46480749 . G GGTGGTGATGGAGCAGCT TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707891G>A None False NM_001145051.2:c.465G>A None None None None None NP_001138523.1:p.(Ala155=) NC_000002.11:g.46707891G>A 2 46707891 . G A NC_000002.12:g.46480752G>A 2 46480752 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707891G>A None MANE NM_001424184.1:c.465G>A None None None None None NP_001411113.1:p.(Ter220XaaextTer?) NC_000002.11:g.46707891G>A 2 46707891 . G A NC_000002.12:g.46480752G>A 2 46480752 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707894G>A None False NM_001145051.2:c.468G>A None None None None None NP_001138523.1:p.(Ala156=) NC_000002.11:g.46707894G>A 2 46707894 . G A NC_000002.12:g.46480755G>A 2 46480755 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707894G>A None MANE NM_001424184.1:c.468G>A None None None None None NP_001411113.1:p.(Ter220XaaextTer?) NC_000002.11:g.46707894G>A 2 46707894 . G A NC_000002.12:g.46480755G>A 2 46480755 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707895C>G None False NM_001145051.2:c.469C>G None None None None None NP_001138523.1:p.(Pro157Ala) NC_000002.11:g.46707895C>G 2 46707895 . C G NC_000002.12:g.46480756C>G 2 46480756 . C G TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707895C>G None MANE NM_001424184.1:c.469C>G None None None None None NP_001411113.1:p.(Pro157Ala) NC_000002.11:g.46707895C>G 2 46707895 . C G NC_000002.12:g.46480756C>G 2 46480756 . C G TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707897C>A None False NM_001145051.2:c.471C>A None None None None None NP_001138523.1:p.(Pro157=) NC_000002.11:g.46707897C>A 2 46707897 . C A NC_000002.12:g.46480758C>A 2 46480758 . C A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46707897C>A None MANE NM_001424184.1:c.471C>A None None None None None NP_001411113.1:p.(Ter220XaaextTer?) NC_000002.11:g.46707897C>A 2 46707897 . C A NC_000002.12:g.46480758C>A 2 46480758 . C A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46711338G>A None False NM_001145051.2:c.478-45G>A NC_000002.11(NM_001145051.2):c.478-45G>A None None None None NP_001138523.1:p.? NC_000002.11:g.46711338G>A 2 46711338 . G A NC_000002.12:g.46484199G>A 2 46484199 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46711338G>A None MANE NM_001424184.1:c.478-45G>A NC_000002.11(NM_001424184.1):c.478-45G>A None None None None NP_001411113.1:p.? NC_000002.11:g.46711338G>A 2 46711338 . G A NC_000002.12:g.46484199G>A 2 46484199 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46711378_46711379delCA VariantSyntaxError: Removing redundant reference bases from variant description False NM_001145051.2:c.478-3_478-2del NC_000002.11(NM_001145051.2):c.478-3_478-2del None None None None NP_001138523.1:p.? NC_000002.11:g.46711380_46711381del 2 46711377 . CCA C NC_000002.12:g.46484241_46484242del 2 46484238 . CCA C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46711378_46711379delCA VariantSyntaxError: Removing redundant reference bases from variant description MANE NM_001424184.1:c.478-3_478-2del NC_000002.11(NM_001424184.1):c.478-3_478-2del None None None None NP_001411113.1:p.? NC_000002.11:g.46711380_46711381del 2 46711377 . CCA C NC_000002.12:g.46484241_46484242del 2 46484238 . CCA C TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46711403C>A None False NM_001145051.2:c.498C>A None None None None None NP_001138523.1:p.(Asn166Lys) NC_000002.11:g.46711403C>A 2 46711403 . C A NC_000002.12:g.46484264C>A 2 46484264 . C A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46711403C>A None MANE NM_001424184.1:c.498C>A None None None None None NP_001411113.1:p.(Asn166Lys) NC_000002.11:g.46711403C>A 2 46711403 . C A NC_000002.12:g.46484264C>A 2 46484264 . C A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46711500G>A None False NM_001145051.2:c.595G>A None None None None None NP_001138523.1:p.(Ala199Thr) NC_000002.11:g.46711500G>A 2 46711500 . G A NC_000002.12:g.46484361G>A 2 46484361 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None -2:g.46711500G>A None MANE NM_001424184.1:c.595G>A None None None None None NP_001411113.1:p.(Ala199Thr) NC_000002.11:g.46711500G>A 2 46711500 . G A NC_000002.12:g.46484361G>A 2 46484361 . G A TMEM247 HGNC:42967 Homo sapiens transmembrane protein 247 (TMEM247), mRNA None