rs193921077
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_013289.4(KIR3DL1):c.809G>A(p.Arg270His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000653 in 1,608,412 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R270S) has been classified as Uncertain significance.
Frequency
Consequence
NM_013289.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KIR3DL1 | NM_013289.4 | c.809G>A | p.Arg270His | missense_variant | 5/9 | ENST00000391728.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KIR3DL1 | ENST00000391728.8 | c.809G>A | p.Arg270His | missense_variant | 5/9 | 1 | NM_013289.4 | P2 | |
KIR3DL1 | ENST00000326542.11 | c.809G>A | p.Arg270His | missense_variant | 5/8 | 1 | A2 | ||
KIR3DL1 | ENST00000358178.4 | c.524G>A | p.Arg175His | missense_variant | 4/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000926 AC: 14AN: 151134Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000124 AC: 19AN: 153704Hom.: 2 AF XY: 0.000168 AC XY: 14AN XY: 83540
GnomAD4 exome AF: 0.0000625 AC: 91AN: 1457164Hom.: 3 Cov.: 35 AF XY: 0.0000745 AC XY: 54AN XY: 724914
GnomAD4 genome ? AF: 0.0000926 AC: 14AN: 151248Hom.: 0 Cov.: 32 AF XY: 0.0000677 AC XY: 5AN XY: 73890
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 30, 2022 | The c.809G>A (p.R270H) alteration is located in exon 5 (coding exon 5) of the KIR3DL1 gene. This alteration results from a G to A substitution at nucleotide position 809, causing the arginine (R) at amino acid position 270 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Malignant tumor of prostate Uncertain:1
Uncertain significance, no assertion criteria provided | literature only | Science for Life laboratory, Karolinska Institutet | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at