rs8190540
Positions:
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_000197.2(HSD17B3):c.386-627_386-626insAGTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.258 in 151,984 control chromosomes in the GnomAD database, including 5,301 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.26 ( 5301 hom., cov: 21)
Consequence
HSD17B3
NM_000197.2 intron
NM_000197.2 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.639
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 -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.3 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSD17B3 | NM_000197.2 | c.386-627_386-626insAGTT | intron_variant | ENST00000375263.8 | |||
SLC35D2-HSD17B3 | NR_182427.1 | n.3153-627_3153-626insAGTT | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD17B3 | ENST00000375263.8 | c.386-627_386-626insAGTT | intron_variant | 1 | NM_000197.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.258 AC: 39236AN: 151866Hom.: 5294 Cov.: 21
GnomAD3 genomes
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39236
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151866
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21
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.258 AC: 39277AN: 151984Hom.: 5301 Cov.: 21 AF XY: 0.252 AC XY: 18722AN XY: 74310
GnomAD4 genome
?
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39277
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151984
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21
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18722
AN XY:
74310
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Asia WGS
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371
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3478
ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at