rs8190569
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_000197.2(HSD17B3):c.823-209A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0154 in 152,304 control chromosomes in the GnomAD database, including 30 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 0.015 ( 30 hom., cov: 31)
Consequence
HSD17B3
NM_000197.2 intron
NM_000197.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.277
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0154 (2351/152304) while in subpopulation NFE AF= 0.0254 (1725/68034). AF 95% confidence interval is 0.0244. There are 30 homozygotes in gnomad4. There are 1105 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 30 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSD17B3 | NM_000197.2 | c.823-209A>C | intron_variant | ENST00000375263.8 | |||
SLC35D2-HSD17B3 | NR_182427.1 | n.3590-209A>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD17B3 | ENST00000375263.8 | c.823-209A>C | intron_variant | 1 | NM_000197.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0154 AC: 2349AN: 152186Hom.: 30 Cov.: 31
GnomAD3 genomes
?
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2349
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152186
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0154 AC: 2351AN: 152304Hom.: 30 Cov.: 31 AF XY: 0.0148 AC XY: 1105AN XY: 74464
GnomAD4 genome
?
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2351
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152304
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31
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1105
AN XY:
74464
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7
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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