rs2072462
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001692.4(ATP6V1B1):c.1002C>T(p.Arg334=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 1,613,544 control chromosomes in the GnomAD database, including 172,005 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. RV334R?) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001692.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6V1B1 | NM_001692.4 | c.1002C>T | p.Arg334= | synonymous_variant | 10/14 | ENST00000234396.10 | |
ATP6V1B1 | XM_011532907.3 | c.1122C>T | p.Arg374= | synonymous_variant | 9/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V1B1 | ENST00000234396.10 | c.1002C>T | p.Arg334= | synonymous_variant | 10/14 | 1 | NM_001692.4 | P1 | |
ATP6V1B1 | ENST00000412314.5 | c.1002C>T | p.Arg334= | synonymous_variant | 10/14 | 5 | |||
VAX2 | ENST00000432367.6 | c.*837-318C>T | intron_variant, NMD_transcript_variant | 5 | |||||
VAX2 | ENST00000646783.1 | c.*890C>T | 3_prime_UTR_variant, NMD_transcript_variant | 11/13 |
Frequencies
GnomAD3 genomes AF: 0.387 AC: 58766AN: 151886Hom.: 12924 Cov.: 32
GnomAD3 exomes AF: 0.477 AC: 119788AN: 251080Hom.: 30220 AF XY: 0.483 AC XY: 65612AN XY: 135770
GnomAD4 exome AF: 0.461 AC: 673324AN: 1461540Hom.: 159081 Cov.: 82 AF XY: 0.464 AC XY: 337564AN XY: 727092
GnomAD4 genome AF: 0.387 AC: 58775AN: 152004Hom.: 12924 Cov.: 32 AF XY: 0.389 AC XY: 28910AN XY: 74274
ClinVar
Submissions by phenotype
not specified Benign:5
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | Arg334Arg in Exon 10 of ATP6V1B1: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wi thin the splice consensus sequence, and has been identified in 44.6% (3132/7020) of European American chromosomes from a broad population by the NHLBI Exome Seq uencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs2072462). - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 09, 2017 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Renal tubular acidosis with progressive nerve deafness Benign:3
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 10, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at