rs7969410
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_012463.4(ATP6V0A2):c.2054G>A(p.Arg685Gln) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.00128 in 1,614,140 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_012463.4 missense, splice_region
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.2054G>A | p.Arg685Gln | missense_variant, splice_region_variant | 16/20 | ENST00000330342.8 | |
ATP6V0A2 | XM_024448911.2 | c.1541G>A | p.Arg514Gln | missense_variant, splice_region_variant | 12/16 | ||
ATP6V0A2 | XM_024448912.2 | c.1232G>A | p.Arg411Gln | missense_variant, splice_region_variant | 9/13 | ||
ATP6V0A2 | XM_024448910.2 | c.1936-1055G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6V0A2 | ENST00000330342.8 | c.2054G>A | p.Arg685Gln | missense_variant, splice_region_variant | 16/20 | 1 | NM_012463.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00672 AC: 1023AN: 152158Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00208 AC: 523AN: 251494Hom.: 5 AF XY: 0.00151 AC XY: 205AN XY: 135922
GnomAD4 exome AF: 0.000721 AC: 1054AN: 1461864Hom.: 7 Cov.: 30 AF XY: 0.000613 AC XY: 446AN XY: 727238
GnomAD4 genome AF: 0.00670 AC: 1020AN: 152276Hom.: 9 Cov.: 32 AF XY: 0.00673 AC XY: 501AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Apr 20, 2015 | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 11, 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. - |
ATP6V0A2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 18, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
ALG9 congenital disorder of glycosylation Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 26, 2024 | - - |
Cutis laxa with osteodystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at