1-119511592-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000862.3(HSD3B1):āc.235A>Gā(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 (ā ). 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