X-40591350-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_005765.3(ATP6AP2):c.285G>A(p.Ser95=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0031 in 1,209,308 control chromosomes in the GnomAD database, including 70 homozygotes. There are 1,049 hemizygotes in GnomAD. 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. S95S) has been classified as Likely benign.
Frequency
Consequence
NM_005765.3 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 |
---|---|---|---|---|---|---|---|
ATP6AP2 | NM_005765.3 | c.285G>A | p.Ser95= | synonymous_variant | 3/9 | ENST00000636580.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ATP6AP2 | ENST00000636580.2 | c.285G>A | p.Ser95= | synonymous_variant | 3/9 | 1 | NM_005765.3 | P3 |
Frequencies
GnomAD3 genomes AF: 0.0155 AC: 1733AN: 112095Hom.: 32 Cov.: 23 AF XY: 0.0141 AC XY: 485AN XY: 34283
GnomAD3 exomes AF: 0.00489 AC: 896AN: 183279Hom.: 19 AF XY: 0.00316 AC XY: 214AN XY: 67735
GnomAD4 exome AF: 0.00183 AC: 2011AN: 1097158Hom.: 38 Cov.: 30 AF XY: 0.00153 AC XY: 556AN XY: 362614
GnomAD4 genome AF: 0.0155 AC: 1741AN: 112150Hom.: 32 Cov.: 23 AF XY: 0.0144 AC XY: 493AN XY: 34348
ClinVar
Submissions by phenotype
not specified Benign:2
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 03, 2013 | 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. - |
Syndromic X-linked intellectual disability Hedera type Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 27, 2018 | - - |
History of neurodevelopmental disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 12, 2014 | General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at