12-10435821-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002260.4(KLRC2):c.166G>A(p.Asp56Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000221 in 1,548,904 control chromosomes in the GnomAD database, including 61 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. D56D) has been classified as Benign.
Frequency
Consequence
NM_002260.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KLRC2 | ENST00000381902.7 | c.166G>A | p.Asp56Asn | missense_variant | Exon 1 of 6 | 1 | NM_002260.4 | ENSP00000371327.2 | ||
ENSG00000255641 | ENST00000539033.1 | c.166G>A | p.Asp56Asn | missense_variant | Exon 1 of 7 | 1 | ENSP00000437563.1 |
Frequencies
GnomAD3 genomes AF: 0.000190 AC: 27AN: 142048Hom.: 7 Cov.: 29
GnomAD3 exomes AF: 0.0000867 AC: 21AN: 242154Hom.: 4 AF XY: 0.0000840 AC XY: 11AN XY: 130942
GnomAD4 exome AF: 0.000225 AC: 316AN: 1406736Hom.: 54 Cov.: 30 AF XY: 0.000194 AC XY: 136AN XY: 700302
GnomAD4 genome AF: 0.000190 AC: 27AN: 142168Hom.: 7 Cov.: 29 AF XY: 0.000202 AC XY: 14AN XY: 69298
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.166G>A (p.D56N) alteration is located in exon 1 (coding exon 1) of the KLRC2 gene. This alteration results from a G to A substitution at nucleotide position 166, causing the aspartic acid (D) at amino acid position 56 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at