rs17883456
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP3BP4_StrongBP6_Very_StrongBA1
The NM_012463.4(ATP6V0A2):c.2438C>T(p.Ala813Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0317 in 1,614,172 control chromosomes in the GnomAD database, including 968 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. A813A) has been classified as Likely benign.
Frequency
Consequence
NM_012463.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6V0A2 | NM_012463.4 | c.2438C>T | p.Ala813Val | missense_variant | 19/20 | ENST00000330342.8 | |
ATP6V0A2 | XM_024448910.2 | c.2318C>T | p.Ala773Val | missense_variant | 18/19 | ||
ATP6V0A2 | XM_024448911.2 | c.1925C>T | p.Ala642Val | missense_variant | 15/16 | ||
ATP6V0A2 | XM_024448912.2 | c.1616C>T | p.Ala539Val | missense_variant | 12/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V0A2 | ENST00000330342.8 | c.2438C>T | p.Ala813Val | missense_variant | 19/20 | 1 | NM_012463.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0251 AC: 3819AN: 152182Hom.: 79 Cov.: 31
GnomAD3 exomes AF: 0.0282 AC: 7088AN: 251488Hom.: 156 AF XY: 0.0289 AC XY: 3930AN XY: 135920
GnomAD4 exome AF: 0.0324 AC: 47368AN: 1461872Hom.: 889 Cov.: 31 AF XY: 0.0322 AC XY: 23386AN XY: 727246
GnomAD4 genome ? AF: 0.0250 AC: 3814AN: 152300Hom.: 79 Cov.: 31 AF XY: 0.0248 AC XY: 1850AN XY: 74468
ClinVar
Submissions by phenotype
not specified Benign:5
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Oct 02, 2013 | - - |
Benign, criteria provided, single submitter | curation | SIB Swiss Institute of Bioinformatics | May 31, 2018 | This variant is interpreted as a Benign - Stand Alone. The following ACMG Tag(s) were applied: BA1 => Allele frequency is >5% in gnomAD (Ashkenazi Jewish population) and about 3% in other populations in Exome Aggregation Consortium. - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
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 | GeneDx | Jan 22, 2016 | 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. - |
ALG9 congenital disorder of glycosylation Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Cutis laxa with osteodystrophy Benign:1
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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at