rs79134187
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_012463.4(ATP6V0A2):āc.1121A>Gā(p.Lys374Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00594 in 1,614,174 control chromosomes in the GnomAD database, including 238 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K374E) has been classified as Uncertain significance.
Frequency
Consequence
NM_012463.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ATP6V0A2 | NM_012463.4 | c.1121A>G | p.Lys374Arg | missense_variant | 10/20 | ENST00000330342.8 | |
ATP6V0A2 | XM_024448910.2 | c.1121A>G | p.Lys374Arg | missense_variant | 10/19 | ||
ATP6V0A2 | XM_024448911.2 | c.608A>G | p.Lys203Arg | missense_variant | 6/16 | ||
ATP6V0A2 | XM_024448912.2 | c.299A>G | p.Lys100Arg | missense_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V0A2 | ENST00000330342.8 | c.1121A>G | p.Lys374Arg | missense_variant | 10/20 | 1 | NM_012463.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0222 AC: 3377AN: 152166Hom.: 104 Cov.: 32
GnomAD3 exomes AF: 0.0113 AC: 2846AN: 251486Hom.: 75 AF XY: 0.00926 AC XY: 1258AN XY: 135914
GnomAD4 exome AF: 0.00425 AC: 6212AN: 1461890Hom.: 134 Cov.: 32 AF XY: 0.00404 AC XY: 2941AN XY: 727246
GnomAD4 genome ? AF: 0.0222 AC: 3380AN: 152284Hom.: 104 Cov.: 32 AF XY: 0.0232 AC XY: 1730AN XY: 74460
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 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. - |
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 10, 2012 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Jun 05, 2015 | - - |
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
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