chr11-30931781-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001387274.1(DCDC1):c.2887C>T(p.Arg963Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.001 in 1,610,008 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001387274.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCDC1 | NM_001387274.1 | c.2887C>T | p.Arg963Trp | missense_variant | 22/39 | ENST00000684477.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCDC1 | ENST00000684477.1 | c.2887C>T | p.Arg963Trp | missense_variant | 22/39 | NM_001387274.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000737 AC: 112AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000505 AC: 124AN: 245526Hom.: 0 AF XY: 0.000414 AC XY: 55AN XY: 132938
GnomAD4 exome AF: 0.00103 AC: 1498AN: 1457878Hom.: 1 Cov.: 30 AF XY: 0.00102 AC XY: 743AN XY: 725222
GnomAD4 genome ? AF: 0.000736 AC: 112AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.000672 AC XY: 50AN XY: 74358
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 09, 2021 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at