rs4746822
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_025130.4(HKDC1):c.63+2687C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,022 control chromosomes in the GnomAD database, including 27,087 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.59 ( 27086 hom., cov: 32)
Exomes 𝑓: 0.38 ( 1 hom. )
Consequence
HKDC1
NM_025130.4 intron
NM_025130.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0290
Genes affected
HKDC1 (HGNC:23302): (hexokinase domain containing 1) This gene encodes a member of the hexokinase protein family. The encoded protein is involved in glucose metabolism, and reduced expression may be associated with gestational diabetes mellitus. High expression of this gene may also be associated with poor prognosis in hepatocarcinoma. [provided by RefSeq, Sep 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.667 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HKDC1 | NM_025130.4 | c.63+2687C>T | intron_variant | ENST00000354624.6 | |||
LOC101928994 | NR_120648.1 | n.326G>A | non_coding_transcript_exon_variant | 3/5 | |||
HKDC1 | XM_011540195.3 | c.63+2687C>T | intron_variant | ||||
HKDC1 | XR_007061989.1 | n.167+2687C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HKDC1 | ENST00000354624.6 | c.63+2687C>T | intron_variant | 1 | NM_025130.4 | P1 | |||
ENST00000450995.1 | n.326G>A | non_coding_transcript_exon_variant | 3/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.585 AC: 88934AN: 151896Hom.: 27052 Cov.: 32
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GnomAD4 exome AF: 0.375 AC: 3AN: 8Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 1AN XY: 2
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GnomAD4 genome ? AF: 0.586 AC: 89014AN: 152014Hom.: 27086 Cov.: 32 AF XY: 0.585 AC XY: 43492AN XY: 74308
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at