rs501999
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001047.4(SRD5A1):c.293+1619T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,692 control chromosomes in the GnomAD database, including 20,948 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 0.52 ( 20948 hom., cov: 33)
Consequence
SRD5A1
NM_001047.4 intron
NM_001047.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.75
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=-0.91).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRD5A1 | NM_001047.4 | c.293+1619T>C | intron_variant | ENST00000274192.7 | |||
SRD5A1 | NM_001324322.2 | c.319+1619T>C | intron_variant | ||||
SRD5A1 | NM_001324323.2 | c.-429+1619T>C | intron_variant | ||||
SRD5A1 | NR_136739.2 | n.430+1619T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRD5A1 | ENST00000274192.7 | c.293+1619T>C | intron_variant | 1 | NM_001047.4 | P1 | |||
SRD5A1 | ENST00000504286.2 | c.293+1619T>C | intron_variant, NMD_transcript_variant | 2 | |||||
SRD5A1 | ENST00000510531.6 | c.293+1619T>C | intron_variant, NMD_transcript_variant | 2 | |||||
SRD5A1 | ENST00000513117.1 | c.293+1619T>C | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.523 AC: 79309AN: 151572Hom.: 20929 Cov.: 33
GnomAD3 genomes
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.523 AC: 79376AN: 151692Hom.: 20948 Cov.: 33 AF XY: 0.521 AC XY: 38589AN XY: 74114
GnomAD4 genome
?
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79376
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33
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38589
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74114
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1532
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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