17-82036724-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_016286.4(DCXR):c.345G>A(p.Ser115Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.134 in 1,613,272 control chromosomes in the GnomAD database, including 23,273 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_016286.4 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCXR | NM_016286.4 | c.345G>A | p.Ser115Ser | synonymous_variant | Exon 4 of 8 | ENST00000306869.7 | NP_057370.1 | |
DCXR | NM_001195218.1 | c.339G>A | p.Ser113Ser | synonymous_variant | Exon 4 of 8 | NP_001182147.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.240 AC: 36521AN: 151862Hom.: 7633 Cov.: 33
GnomAD3 exomes AF: 0.128 AC: 32069AN: 250784Hom.: 4148 AF XY: 0.117 AC XY: 15823AN XY: 135772
GnomAD4 exome AF: 0.123 AC: 179249AN: 1461292Hom.: 15601 Cov.: 34 AF XY: 0.118 AC XY: 85747AN XY: 726930
GnomAD4 genome AF: 0.241 AC: 36615AN: 151980Hom.: 7672 Cov.: 33 AF XY: 0.235 AC XY: 17488AN XY: 74316
ClinVar
Submissions by phenotype
DCXR-related disorder 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