rs142540948
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 3P and 8B. PM2PP2BP4_StrongBS1
The NM_001242896.3(DEPDC5):āc.3241A>Cā(p.Thr1081Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000173 in 1,611,366 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1081I) has been classified as Uncertain significance.
Frequency
Consequence
NM_001242896.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DEPDC5 | NM_001242896.3 | c.3241A>C | p.Thr1081Pro | missense_variant | 32/43 | ENST00000651528.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DEPDC5 | ENST00000651528.2 | c.3241A>C | p.Thr1081Pro | missense_variant | 32/43 | NM_001242896.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000276 AC: 67AN: 242542Hom.: 0 AF XY: 0.000243 AC XY: 32AN XY: 131532
GnomAD4 exome AF: 0.000174 AC: 254AN: 1459088Hom.: 0 Cov.: 30 AF XY: 0.000157 AC XY: 114AN XY: 725436
GnomAD4 genome AF: 0.000164 AC: 25AN: 152278Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74454
ClinVar
Submissions by phenotype
Childhood epilepsy with centrotemporal spikes Pathogenic:1
Pathogenic, no assertion criteria provided | case-control | Bioinformatics Core, Luxembourg Center for Systems Biomedicine | Jan 01, 2017 | CAADphred>15 - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2018 | This alteration is classified as likely 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
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2023 | DEPDC5: BP4 - |
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