rs6201
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000862.3(HSD3B1):c.235A>G(p.Ile79Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0251 in 1,613,244 control chromosomes in the GnomAD database, including 4,875 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000862.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
HSD3B1 | NM_000862.3 | c.235A>G | p.Ile79Val | missense_variant | 3/4 | ENST00000369413.8 | |
HSD3B1 | NM_001328615.1 | c.235A>G | p.Ile79Val | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
HSD3B1 | ENST00000369413.8 | c.235A>G | p.Ile79Val | missense_variant | 3/4 | 1 | NM_000862.3 | P1 | |
HSD3B1 | ENST00000528909.1 | c.235A>G | p.Ile79Val | missense_variant | 2/3 | 1 | P1 | ||
HSD3B1 | ENST00000531340.5 | c.235A>G | p.Ile79Val | missense_variant | 3/3 | 3 | |||
HSD3B1 | ENST00000492140.1 | n.370A>G | non_coding_transcript_exon_variant | 3/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.100 AC: 15216AN: 151994Hom.: 2292 Cov.: 31
GnomAD3 exomes AF: 0.0426 AC: 10670AN: 250476Hom.: 1124 AF XY: 0.0361 AC XY: 4886AN XY: 135402
GnomAD4 exome AF: 0.0173 AC: 25209AN: 1461132Hom.: 2568 Cov.: 31 AF XY: 0.0171 AC XY: 12426AN XY: 726884
GnomAD4 genome ? AF: 0.100 AC: 15276AN: 152112Hom.: 2307 Cov.: 31 AF XY: 0.0977 AC XY: 7269AN XY: 74406
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 13, 2018 | This variant is associated with the following publications: (PMID: 25363768) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at