9-96235628-ATCTTTGTGG-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_000197.2(HSD17B3):c.823-67_823-59del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.469 in 1,336,852 control chromosomes in the GnomAD database, including 149,529 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.43 ( 14699 hom., cov: 0)
Exomes 𝑓: 0.47 ( 134830 hom. )
Consequence
HSD17B3
NM_000197.2 intron
NM_000197.2 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.491
Genes affected
HSD17B3 (HGNC:5212): (hydroxysteroid 17-beta dehydrogenase 3) This isoform of 17 beta-hydroxysteroid dehydrogenase is expressed predominantly in the testis and catalyzes the conversion of androstenedione to testosterone. It preferentially uses NADP as cofactor. Deficiency can result in male pseudohermaphroditism with gynecomastia. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 9-96235628-ATCTTTGTGG-A is Benign according to our data. Variant chr9-96235628-ATCTTTGTGG-A is described in ClinVar as [Benign]. Clinvar id is 1220642.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr9-96235628-ATCTTTGTGG-A is described in Lovd as [Benign].
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.486 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSD17B3 | NM_000197.2 | c.823-67_823-59del | intron_variant | ENST00000375263.8 | NP_000188.1 | |||
SLC35D2-HSD17B3 | NR_182427.1 | n.3590-67_3590-59del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSD17B3 | ENST00000375263.8 | c.823-67_823-59del | intron_variant | 1 | NM_000197.2 | ENSP00000364412 | P1 |
Frequencies
GnomAD3 genomes AF: 0.434 AC: 65751AN: 151486Hom.: 14687 Cov.: 0
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GnomAD4 exome AF: 0.473 AC: 560677AN: 1185246Hom.: 134830 AF XY: 0.474 AC XY: 283934AN XY: 598496
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GnomAD4 genome AF: 0.434 AC: 65784AN: 151606Hom.: 14699 Cov.: 0 AF XY: 0.435 AC XY: 32248AN XY: 74078
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 09, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at