22-31822705-C-G
Variant summary
Our verdict is Benign. The variant received -19 ACMG points: 0P and 19B. BP4_ModerateBP6_Very_StrongBP7BS1BS2
The NM_001242896.3(DEPDC5):c.2019C>G(p.Ser673Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,613,964 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S673S) has been classified as Likely benign.
Frequency
Consequence
NM_001242896.3 synonymous
Scores
Clinical Significance
Conservation
Publications
- epilepsy, familial focal, with variable foci 1Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, Ambry Genetics, Illumina, G2P
- focal epilepsyInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- autosomal dominant epilepsy with auditory featuresInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- autosomal dominant nocturnal frontal lobe epilepsyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- familial focal epilepsy with variable fociInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- Brugada syndromeInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Benign. The variant received -19 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DEPDC5 | ENST00000651528.2 | c.2019C>G | p.Ser673Ser | synonymous_variant | Exon 24 of 43 | NM_001242896.3 | ENSP00000498382.1 | |||
ENSG00000285404 | ENST00000646701.1 | c.1786+3480C>G | intron_variant | Intron 20 of 20 | ENSP00000496158.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000562 AC: 14AN: 249144 AF XY: 0.0000666 show subpopulations
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461774Hom.: 0 Cov.: 30 AF XY: 0.0000550 AC XY: 40AN XY: 727174 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74336 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
not provided Benign:2
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Inborn genetic diseases Benign:1
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
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at