rs80358218
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Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PM4PP5
The ENST00000369416.4(HSD3B2):āc.1119A>Cā(p.Ter373CysextTer95) variant causes a stop lost change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,613,736 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: š 0.0000066 ( 0 hom., cov: 31)
Exomes š: 0.0000075 ( 0 hom. )
Consequence
HSD3B2
ENST00000369416.4 stop_lost
ENST00000369416.4 stop_lost
Scores
2
1
4
Clinical Significance
Conservation
PhyloP100: 3.52
Genes affected
HSD3B2 (HGNC:5218): (hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2) The protein encoded by this gene is a bifunctional enzyme that catalyzes the oxidative conversion of delta(5)-ene-3-beta-hydroxy steroid, and the oxidative conversion of ketosteroids. It plays a crucial role in the biosynthesis of all classes of hormonal steroids. This gene is predominantly expressed in the adrenals and the gonads. Mutations in this gene are associated with 3-beta-hydroxysteroid dehydrogenase, type II, deficiency. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Stoplost variant in ENST00000369416.4 Downstream stopcodon found after 419 codons.
PP5
Variant 1-119422620-A-C is Pathogenic according to our data. Variant chr1-119422620-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 12189.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
HSD3B2 | NM_000198.4 | c.1119A>C | p.Ter373CysextTer95 | stop_lost | 4/4 | ENST00000369416.4 | NP_000189.1 | |
HSD3B2 | NM_001166120.2 | c.1119A>C | p.Ter373CysextTer95 | stop_lost | 4/4 | NP_001159592.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HSD3B2 | ENST00000369416.4 | c.1119A>C | p.Ter373CysextTer95 | stop_lost | 4/4 | 1 | NM_000198.4 | ENSP00000358424 | P1 | |
HSD3B2 | ENST00000543831.5 | c.1119A>C | p.Ter373CysextTer95 | stop_lost | 4/4 | 3 | ENSP00000445122 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000401 AC: 1AN: 249092Hom.: 0 AF XY: 0.00000742 AC XY: 1AN XY: 134794
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GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461538Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727080
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GnomAD4 genome AF: 0.00000657 AC: 1AN: 152198Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74352
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
3 beta-Hydroxysteroid dehydrogenase deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2002 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
A;A
Vest4
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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