X-40605752-T-C
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_005765.3(ATP6AP2):āc.1050T>Cā(p.Asp350Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000251 in 1,201,956 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 82 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_005765.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ATP6AP2 | NM_005765.3 | c.1050T>C | p.Asp350Asp | synonymous_variant | 9/9 | ENST00000636580.2 | NP_005756.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ATP6AP2 | ENST00000636580.2 | c.1050T>C | p.Asp350Asp | synonymous_variant | 9/9 | 1 | NM_005765.3 | ENSP00000490083.1 |
Frequencies
GnomAD3 genomes AF: 0.00133 AC: 149AN: 111961Hom.: 0 Cov.: 23 AF XY: 0.00114 AC XY: 39AN XY: 34123
GnomAD3 exomes AF: 0.000382 AC: 70AN: 183039Hom.: 0 AF XY: 0.000222 AC XY: 15AN XY: 67571
GnomAD4 exome AF: 0.000140 AC: 153AN: 1089943Hom.: 0 Cov.: 29 AF XY: 0.000121 AC XY: 43AN XY: 356295
GnomAD4 genome AF: 0.00133 AC: 149AN: 112013Hom.: 0 Cov.: 23 AF XY: 0.00114 AC XY: 39AN XY: 34185
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 06, 2015 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 17, 2014 | 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 | Labcorp Genetics (formerly Invitae), Labcorp | Jan 30, 2024 | - - |
Syndromic X-linked intellectual disability Hedera type;C3806722:X-linked parkinsonism-spasticity syndrome;C5393313:Congenital disorder of glycosylation, type IIr Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jan 24, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at