rs202226316
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 3P and 12B. PM2PP2BP4_StrongBP6_Very_Strong
The NM_001242896.3(DEPDC5):c.1355C>T(p.Ala452Val) variant causes a missense change. The variant allele was found at a frequency of 0.000247 in 1,613,984 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A452T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001242896.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DEPDC5 | NM_001242896.3 | c.1355C>T | p.Ala452Val | missense_variant | 20/43 | ENST00000651528.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEPDC5 | ENST00000651528.2 | c.1355C>T | p.Ala452Val | missense_variant | 20/43 | NM_001242896.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000197 AC: 30AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000469 AC: 117AN: 249540Hom.: 1 AF XY: 0.000414 AC XY: 56AN XY: 135382
GnomAD4 exome AF: 0.000252 AC: 368AN: 1461886Hom.: 1 Cov.: 32 AF XY: 0.000256 AC XY: 186AN XY: 727244
GnomAD4 genome ? AF: 0.000197 AC: 30AN: 152098Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74306
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 25, 2016 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Familial focal epilepsy with variable foci Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 22, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 30, 2019 | This variant is associated with the following publications: (PMID: 28717674, 23542697, 25366275) - |
Epilepsy, familial focal, with variable foci 1 Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at