rs2286342
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_153717.3(EVC):c.939+10A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.666 in 1,613,168 control chromosomes in the GnomAD database, including 362,604 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_153717.3 intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.663 AC: 100741AN: 151844Hom.: 33920 Cov.: 30
GnomAD3 exomes AF: 0.621 AC: 156079AN: 251244Hom.: 49870 AF XY: 0.624 AC XY: 84739AN XY: 135796
GnomAD4 exome AF: 0.667 AC: 973956AN: 1461206Hom.: 328661 Cov.: 41 AF XY: 0.664 AC XY: 482989AN XY: 726946
GnomAD4 genome AF: 0.664 AC: 100830AN: 151962Hom.: 33943 Cov.: 30 AF XY: 0.657 AC XY: 48843AN XY: 74292
ClinVar
Submissions by phenotype
Ellis-van Creveld syndrome Benign:4
- -
- -
- -
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
not specified Benign:3
- -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
- -
Ellis-van Creveld syndrome;C0457013:Curry-Hall syndrome Benign:1
- -
not provided Benign:1
- -
Curry-Hall syndrome Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at