chr11-30952568-C-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001387274.1(DCDC1):c.2592G>T(p.Arg864Ser) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,273,900 control chromosomes in the GnomAD database, including 7,884 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/14 in silico tools predict a benign outcome for this variant. 2/2 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001387274.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCDC1 | NM_001387274.1 | c.2592G>T | p.Arg864Ser | missense_variant, splice_region_variant | 21/39 | ENST00000684477.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCDC1 | ENST00000684477.1 | c.2592G>T | p.Arg864Ser | missense_variant, splice_region_variant | 21/39 | NM_001387274.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.101 AC: 15319AN: 151834Hom.: 954 Cov.: 32
GnomAD3 exomes AF: 0.132 AC: 25049AN: 189408Hom.: 2042 AF XY: 0.128 AC XY: 13227AN XY: 103146
GnomAD4 exome AF: 0.103 AC: 115266AN: 1121952Hom.: 6930 Cov.: 14 AF XY: 0.103 AC XY: 58458AN XY: 566366
GnomAD4 genome ? AF: 0.101 AC: 15323AN: 151948Hom.: 954 Cov.: 32 AF XY: 0.105 AC XY: 7787AN XY: 74244
ClinVar
Submissions by phenotype
DCDC1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 25, 2019 | 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). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at