rs2735059
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_017010810.1(HLA-F):c.1279G>A(p.Glu427Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.421 in 518,512 control chromosomes in the GnomAD database, including 47,342 homozygotes. In-silico tool predicts a benign outcome for this variant. 4/4 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
XM_017010810.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HLA-F | XM_017010810.1 | c.1279G>A | p.Glu427Lys | missense_variant | 8/8 | XP_016866299.1 | ||
HLA-F | XM_047418718.1 | c.1158+1073G>A | intron_variant | XP_047274674.1 | ||||
HLA-F | XM_047418719.1 | c.1125+1073G>A | intron_variant | XP_047274675.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HLA-F | ENST00000475996.1 | c.*14G>A | 3_prime_UTR_variant | 2/2 | 6 | ENSP00000486309.1 | ||||
HLA-F | ENST00000465459.2 | c.403+2034G>A | intron_variant | 6 | ENSP00000486947.1 | |||||
HLA-F-AS1 | ENST00000399247.6 | n.1366+288C>T | intron_variant | 6 |
Frequencies
GnomAD3 genomes AF: 0.424 AC: 64489AN: 152000Hom.: 13765 Cov.: 32
GnomAD3 exomes AF: 0.422 AC: 96443AN: 228538Hom.: 20861 AF XY: 0.418 AC XY: 52770AN XY: 126338
GnomAD4 exome AF: 0.420 AC: 153810AN: 366396Hom.: 33561 Cov.: 0 AF XY: 0.411 AC XY: 86301AN XY: 210090
GnomAD4 genome AF: 0.424 AC: 64539AN: 152116Hom.: 13781 Cov.: 32 AF XY: 0.423 AC XY: 31433AN XY: 74348
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at