rs3736316
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The ENST00000274192.7(SRD5A1):c.480G>A(p.Thr160=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 1,611,670 control chromosomes in the GnomAD database, including 106,769 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.35 ( 9402 hom., cov: 32)
Exomes 𝑓: 0.36 ( 97367 hom. )
Consequence
SRD5A1
ENST00000274192.7 synonymous
ENST00000274192.7 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.27
Genes affected
SRD5A1 (HGNC:11284): (steroid 5 alpha-reductase 1) Steroid 5-alpha-reductase (EC 1.3.99.5) catalyzes the conversion of testosterone into the more potent androgen, dihydrotestosterone (DHT). Also see SRD5A2 (MIM 607306).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP7
Synonymous conserved (PhyloP=-2.27 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRD5A1 | NM_001047.4 | c.480G>A | p.Thr160= | synonymous_variant | 3/5 | ENST00000274192.7 | NP_001038.1 | |
SRD5A1 | NM_001324322.2 | c.339G>A | p.Thr113= | synonymous_variant | 2/4 | NP_001311251.1 | ||
SRD5A1 | NM_001324323.2 | c.261G>A | p.Thr87= | synonymous_variant | 4/6 | NP_001311252.1 | ||
SRD5A1 | NR_136739.2 | n.807G>A | non_coding_transcript_exon_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRD5A1 | ENST00000274192.7 | c.480G>A | p.Thr160= | synonymous_variant | 3/5 | 1 | NM_001047.4 | ENSP00000274192 | P1 | |
SRD5A1 | ENST00000504286.2 | c.670G>A | p.Gly224Arg | missense_variant, NMD_transcript_variant | 4/6 | 2 | ENSP00000518753 | |||
SRD5A1 | ENST00000513117.1 | c.313G>A | p.Gly105Arg | missense_variant, NMD_transcript_variant | 2/4 | 2 | ENSP00000421342 | |||
SRD5A1 | ENST00000510531.6 | c.*601G>A | 3_prime_UTR_variant, NMD_transcript_variant | 4/6 | 2 | ENSP00000425330 |
Frequencies
GnomAD3 genomes AF: 0.348 AC: 52794AN: 151758Hom.: 9390 Cov.: 32
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GnomAD3 exomes AF: 0.330 AC: 82832AN: 250758Hom.: 14468 AF XY: 0.328 AC XY: 44474AN XY: 135554
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GnomAD4 exome AF: 0.359 AC: 524465AN: 1459794Hom.: 97367 Cov.: 33 AF XY: 0.356 AC XY: 258299AN XY: 726234
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GnomAD4 genome AF: 0.348 AC: 52846AN: 151876Hom.: 9402 Cov.: 32 AF XY: 0.342 AC XY: 25363AN XY: 74222
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at