11-30899596-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP3BP6BP7BA1
The NM_001387274.1(DCDC1):c.4710G>A(p.Lys1570Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00373 in 1,578,370 control chromosomes in the GnomAD database, including 176 homozygotes. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001387274.1 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCDC1 | NM_001387274.1 | c.4710G>A | p.Lys1570Lys | synonymous_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.4710G>A | p.Lys1570Lys | synonymous_variant | Exon 34 of 39 | NM_001387274.1 | ENSP00000507427.1 |
Frequencies
GnomAD3 genomes AF: 0.0181 AC: 2753AN: 151976Hom.: 85 Cov.: 32
GnomAD3 exomes AF: 0.00515 AC: 1127AN: 219046Hom.: 18 AF XY: 0.00418 AC XY: 494AN XY: 118100
GnomAD4 exome AF: 0.00219 AC: 3129AN: 1426276Hom.: 90 Cov.: 30 AF XY: 0.00222 AC XY: 1569AN XY: 707450
GnomAD4 genome AF: 0.0181 AC: 2759AN: 152094Hom.: 86 Cov.: 32 AF XY: 0.0177 AC XY: 1319AN XY: 74358
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). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at