chr10-69300878-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001358263.1(HK1):c.75+5198G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.912 in 1,335,008 control chromosomes in the GnomAD database, including 556,048 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.90 ( 61848 hom., cov: 31)
Exomes 𝑓: 0.91 ( 494200 hom. )
Consequence
HK1
NM_001358263.1 intron
NM_001358263.1 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.27
Genes affected
HK1 (HGNC:4922): (hexokinase 1) Hexokinases phosphorylate glucose to produce glucose-6-phosphate, the first step in most glucose metabolism pathways. This gene encodes a ubiquitous form of hexokinase which localizes to the outer membrane of mitochondria. Mutations in this gene have been associated with hemolytic anemia due to hexokinase deficiency. Alternative splicing of this gene results in several transcript variants which encode different isoforms, some of which are tissue-specific. [provided by RefSeq, Apr 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-1.02).
BP6
?
Variant 10-69300878-G-A is Benign according to our data. Variant chr10-69300878-G-A is described in ClinVar as [Benign]. Clinvar id is 994063.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr10-69300878-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HK1 | NM_001358263.1 | c.75+5198G>A | intron_variant | ENST00000643399.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HK1 | ENST00000643399.2 | c.75+5198G>A | intron_variant | NM_001358263.1 |
Frequencies
GnomAD3 genomes ? AF: 0.901 AC: 136922AN: 152040Hom.: 61798 Cov.: 31
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GnomAD3 exomes AF: 0.910 AC: 206473AN: 226846Hom.: 94166 AF XY: 0.911 AC XY: 111498AN XY: 122424
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GnomAD4 exome AF: 0.914 AC: 1080783AN: 1182850Hom.: 494200 Cov.: 15 AF XY: 0.913 AC XY: 548232AN XY: 600408
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GnomAD4 genome ? AF: 0.901 AC: 137029AN: 152158Hom.: 61848 Cov.: 31 AF XY: 0.901 AC XY: 67014AN XY: 74374
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:2
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Nov 30, 2023 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at