chr1-119415424-G-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_000198.4(HSD3B2):c.5G>T(p.Gly2Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000293 in 1,613,908 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G2G) 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 -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSD3B2 | NM_000198.4 | c.5G>T | p.Gly2Val | missense_variant | 2/4 | ENST00000369416.4 | |
HSD3B2 | NM_001166120.2 | c.5G>T | p.Gly2Val | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD3B2 | ENST00000369416.4 | c.5G>T | p.Gly2Val | missense_variant | 2/4 | 1 | NM_000198.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00146 AC: 222AN: 152156Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000414 AC: 104AN: 251080Hom.: 0 AF XY: 0.000413 AC XY: 56AN XY: 135690
GnomAD4 exome AF: 0.000171 AC: 250AN: 1461634Hom.: 1 Cov.: 31 AF XY: 0.000146 AC XY: 106AN XY: 727126
GnomAD4 genome ? AF: 0.00146 AC: 223AN: 152274Hom.: 1 Cov.: 32 AF XY: 0.00136 AC XY: 101AN XY: 74450
ClinVar
Submissions by phenotype
HSD3B2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 31, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
not provided Benign:1
Likely 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