chr7-82066526-TAA-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1
The NM_000722.4(CACNA2D1):c.659-4_659-3delTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0299 in 1,348,660 control chromosomes in the GnomAD database, including 56 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000722.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0210 AC: 2346AN: 111648Hom.: 55 Cov.: 27
GnomAD3 exomes AF: 0.0775 AC: 7016AN: 90532Hom.: 3 AF XY: 0.0777 AC XY: 3771AN XY: 48522
GnomAD4 exome AF: 0.0306 AC: 37912AN: 1237034Hom.: 1 AF XY: 0.0318 AC XY: 19387AN XY: 610022
GnomAD4 genome AF: 0.0210 AC: 2347AN: 111626Hom.: 55 Cov.: 27 AF XY: 0.0212 AC XY: 1124AN XY: 52912
ClinVar
Submissions by phenotype
not specified Benign:2
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not provided Benign:1
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Cardiovascular phenotype Benign:1
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
CACNA2D1-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