rs782158864
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Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_004493.3(HSD17B10):c.144G>A(p.Glu48=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000662 in 1,208,639 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.000026 ( 0 hom., 1 hem., cov: 25)
Exomes 𝑓: 0.0000046 ( 0 hom. 2 hem. )
Consequence
HSD17B10
NM_004493.3 synonymous
NM_004493.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.723
Genes affected
HSD17B10 (HGNC:4800): (hydroxysteroid 17-beta dehydrogenase 10) This gene encodes 3-hydroxyacyl-CoA dehydrogenase type II, a member of the short-chain dehydrogenase/reductase superfamily. The gene product is a mitochondrial protein that catalyzes the oxidation of a wide variety of fatty acids and steroids, and is a subunit of mitochondrial ribonuclease P, which is involved in tRNA maturation. The protein has been implicated in the development of Alzheimer disease, and mutations in the gene are the cause of 17beta-hydroxysteroid dehydrogenase type 10 (HSD10) deficiency. Several alternatively spliced transcript variants have been identified, but the full-length nature of only two transcript variants has been determined. [provided by RefSeq, Aug 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -17 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
?
Variant X-53433770-C-T is Benign according to our data. Variant chrX-53433770-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 435469.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-0.723 with no splicing effect.
BS2
?
High Hemizygotes in GnomAdExome4 at 2 XL gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSD17B10 | NM_004493.3 | c.144G>A | p.Glu48= | synonymous_variant | 2/6 | ENST00000168216.11 | |
HSD17B10 | NM_001037811.2 | c.144G>A | p.Glu48= | synonymous_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD17B10 | ENST00000168216.11 | c.144G>A | p.Glu48= | synonymous_variant | 2/6 | 1 | NM_004493.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000265 AC: 3AN: 113284Hom.: 0 Cov.: 25 AF XY: 0.0000282 AC XY: 1AN XY: 35416
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GnomAD3 exomes AF: 0.0000174 AC: 3AN: 172371Hom.: 0 AF XY: 0.0000169 AC XY: 1AN XY: 59031
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GnomAD4 exome AF: 0.00000456 AC: 5AN: 1095355Hom.: 0 Cov.: 31 AF XY: 0.00000554 AC XY: 2AN XY: 361087
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GnomAD4 genome ? AF: 0.0000265 AC: 3AN: 113284Hom.: 0 Cov.: 25 AF XY: 0.0000282 AC XY: 1AN XY: 35416
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Jan 11, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
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Name
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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