1-119512152-A-G
Variant names:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_000862.3(HSD3B1):c.310+485A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.78 in 152,128 control chromosomes in the GnomAD database, including 46,852 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 0.78 ( 46852 hom., cov: 32)
Consequence
HSD3B1
NM_000862.3 intron
NM_000862.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0620
Genes affected
HSD3B1 (HGNC:5217): (hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1) The protein encoded by this gene is an enzyme that catalyzes the oxidative conversion of delta-5-3-beta-hydroxysteroid precursors into delta-4-ketosteroids, which leads to the production of all classes of steroid hormones. The encoded protein also catalyzes the interconversion of 3-beta-hydroxy- and 3-keto-5-alpha-androstane steroids. [provided by RefSeq, Jun 2016]
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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=-1.02).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSD3B1 | ENST00000369413.8 | c.310+485A>G | intron_variant | Intron 3 of 3 | 1 | NM_000862.3 | ENSP00000358421.3 | |||
HSD3B1 | ENST00000528909.1 | c.310+485A>G | intron_variant | Intron 2 of 2 | 1 | ENSP00000432268.1 | ||||
HSD3B1 | ENST00000492140.1 | n.*200A>G | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.780 AC: 118571AN: 152010Hom.: 46805 Cov.: 32
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.780 AC: 118675AN: 152128Hom.: 46852 Cov.: 32 AF XY: 0.786 AC XY: 58481AN XY: 74366
GnomAD4 genome
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32
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58481
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74366
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3049
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3476
ClinVar
Not reported inComputational 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