chr5-6633666-C-G
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001047.4(SRD5A1):c.90C>G(p.Arg30=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.549 in 1,579,142 control chromosomes in the GnomAD database, including 239,443 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.57 ( 25380 hom., cov: 35)
Exomes 𝑓: 0.55 ( 214063 hom. )
Consequence
SRD5A1
NM_001047.4 synonymous
NM_001047.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.446
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 -15 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
Variant 5-6633666-C-G is Benign according to our data. Variant chr5-6633666-C-G is described in ClinVar as [Benign]. Clinvar id is 1255175.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.446 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRD5A1 | NM_001047.4 | c.90C>G | p.Arg30= | synonymous_variant | 1/5 | ENST00000274192.7 | |
SRD5A1 | NM_001324322.2 | c.116C>G | p.Ala39Gly | missense_variant | 1/4 | ||
SRD5A1 | NM_001324323.2 | c.-632C>G | 5_prime_UTR_variant | 1/6 | |||
SRD5A1 | NR_136739.2 | n.227C>G | non_coding_transcript_exon_variant | 1/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRD5A1 | ENST00000274192.7 | c.90C>G | p.Arg30= | synonymous_variant | 1/5 | 1 | NM_001047.4 | P1 | |
SRD5A1 | ENST00000504286.2 | c.90C>G | p.Arg30= | synonymous_variant, NMD_transcript_variant | 1/6 | 2 | |||
SRD5A1 | ENST00000513117.1 | c.90C>G | p.Arg30= | synonymous_variant, NMD_transcript_variant | 1/4 | 2 | |||
SRD5A1 | ENST00000510531.6 | c.90C>G | p.Arg30= | synonymous_variant, NMD_transcript_variant | 1/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.574 AC: 87183AN: 151970Hom.: 25361 Cov.: 35
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GnomAD3 exomes AF: 0.547 AC: 104315AN: 190608Hom.: 28774 AF XY: 0.543 AC XY: 57813AN XY: 106504
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GnomAD4 exome AF: 0.546 AC: 779586AN: 1427056Hom.: 214063 Cov.: 68 AF XY: 0.545 AC XY: 385981AN XY: 708792
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GnomAD4 genome ? AF: 0.574 AC: 87258AN: 152086Hom.: 25380 Cov.: 35 AF XY: 0.571 AC XY: 42462AN XY: 74372
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 11, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at