chr2-74873281-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_ModerateBP6BP7
The NM_000189.5(HK2):c.501C>T(p.Phe167Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000337 in 1,612,806 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_000189.5 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000368 AC: 56AN: 152196Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000414 AC: 104AN: 251496Hom.: 0 AF XY: 0.000493 AC XY: 67AN XY: 135922
GnomAD4 exome AF: 0.000333 AC: 487AN: 1460492Hom.: 1 Cov.: 30 AF XY: 0.000354 AC XY: 257AN XY: 726624
GnomAD4 genome AF: 0.000368 AC: 56AN: 152314Hom.: 1 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74476
ClinVar
Submissions by phenotype
HK2-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