19-54742227-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015868.3(KIR2DL3):āc.318C>Gā(p.His106Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000663 in 1,614,186 control chromosomes in the GnomAD database, including 1 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 Uncertain significance (ā ).
Frequency
Consequence
NM_015868.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIR2DL3 | NM_015868.3 | c.318C>G | p.His106Gln | missense_variant | 3/8 | ENST00000342376.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIR2DL3 | ENST00000342376.4 | c.318C>G | p.His106Gln | missense_variant | 3/8 | 1 | NM_015868.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152186Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000843 AC: 11AN: 130528Hom.: 3 AF XY: 0.000116 AC XY: 8AN XY: 68752
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461882Hom.: 0 Cov.: 39 AF XY: 0.0000825 AC XY: 60AN XY: 727244
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152304Hom.: 1 Cov.: 32 AF XY: 0.0000671 AC XY: 5AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 08, 2023 | The c.318C>G (p.H106Q) alteration is located in exon 3 (coding exon 3) of the KIR2DL3 gene. This alteration results from a C to G substitution at nucleotide position 318, causing the histidine (H) at amino acid position 106 to be replaced by a glutamine (Q). 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