chr1-119422001-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_000198.4(HSD3B2):c.500C>T(p.Ala167Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00122 in 1,614,062 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. A167A) has been classified as Likely benign.
Frequency
Consequence
NM_000198.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSD3B2 | NM_000198.4 | c.500C>T | p.Ala167Val | missense_variant | 4/4 | ENST00000369416.4 | |
HSD3B2 | NM_001166120.2 | c.500C>T | p.Ala167Val | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD3B2 | ENST00000369416.4 | c.500C>T | p.Ala167Val | missense_variant | 4/4 | 1 | NM_000198.4 | P1 | |
HSD3B2 | ENST00000543831.5 | c.500C>T | p.Ala167Val | missense_variant | 4/4 | 3 | P1 | ||
HSD3B2 | ENST00000433745.5 | c.500C>T | p.Ala167Val | missense_variant | 4/4 | 3 | |||
HSD3B2 | ENST00000448448.2 | n.444C>T | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000966 AC: 147AN: 152112Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00142 AC: 357AN: 251122Hom.: 2 AF XY: 0.00153 AC XY: 208AN XY: 135720
GnomAD4 exome AF: 0.00125 AC: 1821AN: 1461832Hom.: 6 Cov.: 31 AF XY: 0.00138 AC XY: 1000AN XY: 727224
GnomAD4 genome AF: 0.000966 AC: 147AN: 152230Hom.: 0 Cov.: 31 AF XY: 0.00103 AC XY: 77AN XY: 74450
ClinVar
Submissions by phenotype
3 beta-Hydroxysteroid dehydrogenase deficiency Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Pars Genome Lab | May 18, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Dec 09, 2019 | - - |
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden | Nov 03, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at