11-30899619-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001387274.1(DCDC1):c.4687G>A(p.Glu1563Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0107 in 1,567,600 control chromosomes in the GnomAD database, including 94 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001387274.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCDC1 | NM_001387274.1 | c.4687G>A | p.Glu1563Lys | missense_variant | Exon 34 of 39 | ENST00000684477.1 | NP_001374203.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCDC1 | ENST00000684477.1 | c.4687G>A | p.Glu1563Lys | missense_variant | Exon 34 of 39 | NM_001387274.1 | ENSP00000507427.1 |
Frequencies
GnomAD3 genomes AF: 0.00853 AC: 1297AN: 152004Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00752 AC: 1499AN: 199286Hom.: 4 AF XY: 0.00795 AC XY: 850AN XY: 106860
GnomAD4 exome AF: 0.0109 AC: 15446AN: 1415478Hom.: 85 Cov.: 30 AF XY: 0.0109 AC XY: 7653AN XY: 701212
GnomAD4 genome AF: 0.00853 AC: 1297AN: 152122Hom.: 9 Cov.: 32 AF XY: 0.00828 AC XY: 616AN XY: 74380
ClinVar
Submissions by phenotype
DCDC5-related condition Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
DCDC1: BP4, BS1, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at