rs874556
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_025130.4(HKDC1):āc.371C>Gā(p.Thr124Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000132 in 152,022 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T124I) has been classified as Likely benign.
Frequency
Consequence
NM_025130.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HKDC1 | NM_025130.4 | c.371C>G | p.Thr124Arg | missense_variant | 3/18 | ENST00000354624.6 | |
HKDC1 | XM_011540195.3 | c.371C>G | p.Thr124Arg | missense_variant | 3/16 | ||
HKDC1 | XR_007061989.1 | n.475C>G | non_coding_transcript_exon_variant | 3/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HKDC1 | ENST00000354624.6 | c.371C>G | p.Thr124Arg | missense_variant | 3/18 | 1 | NM_025130.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152022Hom.: 0 Cov.: 32
GnomAD4 exome Cov.: 60
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152022Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74254
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at