rs1560149
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001047.4(SRD5A1):c.293+1823C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,266 control chromosomes in the GnomAD database, including 3,285 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 0.19 ( 3285 hom., cov: 35)
Consequence
SRD5A1
NM_001047.4 intron
NM_001047.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.603
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.472 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRD5A1 | NM_001047.4 | c.293+1823C>G | intron_variant | ENST00000274192.7 | NP_001038.1 | |||
SRD5A1 | NM_001324322.2 | c.319+1823C>G | intron_variant | NP_001311251.1 | ||||
SRD5A1 | NM_001324323.2 | c.-429+1823C>G | intron_variant | NP_001311252.1 | ||||
SRD5A1 | NR_136739.2 | n.430+1823C>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SRD5A1 | ENST00000274192.7 | c.293+1823C>G | intron_variant | 1 | NM_001047.4 | ENSP00000274192 | P1 | |||
SRD5A1 | ENST00000504286.2 | c.293+1823C>G | intron_variant, NMD_transcript_variant | 2 | ENSP00000518753 | |||||
SRD5A1 | ENST00000510531.6 | c.293+1823C>G | intron_variant, NMD_transcript_variant | 2 | ENSP00000425330 | |||||
SRD5A1 | ENST00000513117.1 | c.293+1823C>G | intron_variant, NMD_transcript_variant | 2 | ENSP00000421342 |
Frequencies
GnomAD3 genomes AF: 0.190 AC: 28851AN: 152148Hom.: 3285 Cov.: 35
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.189 AC: 28852AN: 152266Hom.: 3285 Cov.: 35 AF XY: 0.194 AC XY: 14469AN XY: 74446
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1109
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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