rs2229629
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The ENST00000290573.7(HK2):c.2531G>A(p.Arg844Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0445 in 1,613,952 control chromosomes in the GnomAD database, including 12,294 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 Benign (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
ENST00000290573.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HK2 | NM_000189.5 | c.2531G>A | p.Arg844Lys | missense_variant | 17/18 | ENST00000290573.7 | NP_000180.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HK2 | ENST00000290573.7 | c.2531G>A | p.Arg844Lys | missense_variant | 17/18 | 1 | NM_000189.5 | ENSP00000290573 | P1 | |
HK2 | ENST00000409174.1 | c.2447G>A | p.Arg816Lys | missense_variant | 17/18 | 1 | ENSP00000387140 |
Frequencies
GnomAD3 genomes AF: 0.169 AC: 25638AN: 152064Hom.: 6210 Cov.: 32
GnomAD3 exomes AF: 0.0605 AC: 15183AN: 251106Hom.: 2697 AF XY: 0.0504 AC XY: 6844AN XY: 135748
GnomAD4 exome AF: 0.0315 AC: 46057AN: 1461770Hom.: 6068 Cov.: 32 AF XY: 0.0299 AC XY: 21716AN XY: 727198
GnomAD4 genome AF: 0.169 AC: 25698AN: 152182Hom.: 6226 Cov.: 32 AF XY: 0.164 AC XY: 12214AN XY: 74412
ClinVar
Submissions by phenotype
HK2-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 06, 2019 | This variant is classified as 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