12-10433880-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_002260.4(KLRC2):c.394G>A(p.Gly132Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000245 in 1,550,410 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_002260.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000148 AC: 21AN: 141882Hom.: 5 Cov.: 27
GnomAD3 exomes AF: 0.0000454 AC: 11AN: 242186Hom.: 4 AF XY: 0.0000534 AC XY: 7AN XY: 130968
GnomAD4 exome AF: 0.0000121 AC: 17AN: 1408528Hom.: 3 Cov.: 30 AF XY: 0.0000128 AC XY: 9AN XY: 701126
GnomAD4 genome AF: 0.000148 AC: 21AN: 141882Hom.: 5 Cov.: 27 AF XY: 0.000159 AC XY: 11AN XY: 69084
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at