rs1047303
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000862.3(HSD3B1):c.1100C>A(p.Thr367Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 1,613,074 control chromosomes in the GnomAD database, including 412,097 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign,drug response (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_000862.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.764 AC: 115773AN: 151570Hom.: 44897 Cov.: 29
GnomAD3 exomes AF: 0.755 AC: 188429AN: 249654Hom.: 72300 AF XY: 0.748 AC XY: 100974AN XY: 134938
GnomAD4 exome AF: 0.705 AC: 1030890AN: 1461386Hom.: 367156 Cov.: 61 AF XY: 0.707 AC XY: 513679AN XY: 726994
GnomAD4 genome AF: 0.764 AC: 115875AN: 151688Hom.: 44941 Cov.: 29 AF XY: 0.771 AC XY: 57102AN XY: 74092
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2020 | This variant is associated with the following publications: (PMID: 31932420) - |
Androgen deprivation therapy response Other:1
drug response, criteria provided, single submitter | clinical testing;research | Desai Sethi Urology Institute, University Of Miami | Mar 01, 2024 | Slower development of castration-resistant prostate cancer has now been shown in at least 10 cohorts (Hearn, et al. Lancet Oncol. 2016 (PMID:27575027); Hearn, et al. JAMA Oncol. 2018 (PMID:29049492); Agarwal, et al. JAMA Oncol. 2017 (PMID:28208175)) and has shown to result in higher prostate cancer specific mortality rates in a cohort of over 5,000 patients (McKay, et al. JAMA Netw Open. 2024 (PMID:38506808)). More Responsive |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at