19-54783763-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_014218.3(KIR2DL1):c.997A>G(p.Thr333Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 1,604,402 control chromosomes in the GnomAD database, including 2,106 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_014218.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIR2DL1 | ENST00000336077.11 | c.997A>G | p.Thr333Ala | missense_variant | Exon 8 of 8 | 1 | NM_014218.3 | ENSP00000336769.5 | ||
KIR2DL1 | ENST00000291633.7 | c.1075A>G | p.Thr359Ala | missense_variant | Exon 9 of 9 | 1 | ENSP00000291633.7 | |||
ENSG00000215765 | ENST00000400864.3 | n.72-2700A>G | intron_variant | Intron 2 of 5 | 5 |
Frequencies
GnomAD3 genomes AF: 0.153 AC: 23003AN: 150592Hom.: 252 Cov.: 33
GnomAD4 exome AF: 0.148 AC: 215318AN: 1453690Hom.: 1852 Cov.: 71 AF XY: 0.153 AC XY: 110547AN XY: 723368
GnomAD4 genome AF: 0.153 AC: 23023AN: 150712Hom.: 254 Cov.: 33 AF XY: 0.155 AC XY: 11417AN XY: 73620
ClinVar
Submissions by phenotype
KIR2DL1-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at