chr5-6662832-C-T
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Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1
The NM_001047.4(SRD5A1):c.579C>T(p.Tyr193=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00453 in 1,612,340 control chromosomes in the GnomAD database, including 281 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.024 ( 156 hom., cov: 33)
Exomes 𝑓: 0.0025 ( 125 hom. )
Consequence
SRD5A1
NM_001047.4 synonymous
NM_001047.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.382
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=-0.65).
BP6
Variant 5-6662832-C-T is Benign according to our data. Variant chr5-6662832-C-T is described in ClinVar as [Benign]. Clinvar id is 767993.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.382 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0792 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRD5A1 | NM_001047.4 | c.579C>T | p.Tyr193= | synonymous_variant | 4/5 | ENST00000274192.7 | |
SRD5A1 | NM_001324322.2 | c.438C>T | p.Tyr146= | synonymous_variant | 3/4 | ||
SRD5A1 | NM_001324323.2 | c.360C>T | p.Tyr120= | synonymous_variant | 5/6 | ||
SRD5A1 | NR_136739.2 | n.906C>T | non_coding_transcript_exon_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRD5A1 | ENST00000274192.7 | c.579C>T | p.Tyr193= | synonymous_variant | 4/5 | 1 | NM_001047.4 | P1 | |
SRD5A1 | ENST00000504286.2 | c.*4C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/6 | 2 | ||||
SRD5A1 | ENST00000510531.6 | c.*700C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/6 | 2 | ||||
SRD5A1 | ENST00000513117.1 | c.*4C>T | 3_prime_UTR_variant, NMD_transcript_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0237 AC: 3610AN: 152134Hom.: 154 Cov.: 33
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GnomAD3 exomes AF: 0.00621 AC: 1561AN: 251328Hom.: 63 AF XY: 0.00469 AC XY: 637AN XY: 135850
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GnomAD4 exome AF: 0.00253 AC: 3692AN: 1460088Hom.: 125 Cov.: 31 AF XY: 0.00220 AC XY: 1601AN XY: 726336
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GnomAD4 genome AF: 0.0238 AC: 3616AN: 152252Hom.: 156 Cov.: 33 AF XY: 0.0232 AC XY: 1729AN XY: 74438
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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 | Invitae | Jun 06, 2018 | - - |
Computational scores
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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