19-54727748-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_153443.5(KIR3DL3):āc.493T>Gā(p.Leu165Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,612,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_153443.5 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIR3DL3 | NM_153443.5 | c.493T>G | p.Leu165Val | missense_variant | 4/8 | ENST00000291860.2 | NP_703144.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIR3DL3 | ENST00000291860.2 | c.493T>G | p.Leu165Val | missense_variant | 4/8 | 1 | NM_153443.5 | ENSP00000291860.1 | ||
ENSG00000215765 | ENST00000400864.3 | n.35+3218T>G | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00000662 AC: 1AN: 151074Hom.: 0 Cov.: 27
GnomAD3 exomes AF: 0.000202 AC: 37AN: 182716Hom.: 13 AF XY: 0.000305 AC XY: 30AN XY: 98500
GnomAD4 exome AF: 0.0000513 AC: 75AN: 1461782Hom.: 0 Cov.: 53 AF XY: 0.0000729 AC XY: 53AN XY: 727210
GnomAD4 genome AF: 0.00000662 AC: 1AN: 151074Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 73654
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 19, 2024 | The c.493T>G (p.L165V) alteration is located in exon 4 (coding exon 4) of the KIR3DL3 gene. This alteration results from a T to G substitution at nucleotide position 493, causing the leucine (L) at amino acid position 165 to be replaced by a valine (V). 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