chr4-55369693-T-C
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_024592.5(SRD5A3):c.698-139T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 980,510 control chromosomes in the GnomAD database, including 43,148 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.28 ( 6226 hom., cov: 29)
Exomes 𝑓: 0.29 ( 36922 hom. )
Consequence
SRD5A3
NM_024592.5 intron
NM_024592.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.766
Genes affected
SRD5A3 (HGNC:25812): (steroid 5 alpha-reductase 3) The protein encoded by this gene belongs to the steroid 5-alpha reductase family, and polyprenol reductase subfamily. It is involved in the production of androgen 5-alpha-dihydrotestosterone (DHT) from testosterone, and maintenance of the androgen-androgen receptor activation pathway. This protein is also necessary for the conversion of polyprenol into dolichol, which is required for the synthesis of dolichol-linked monosaccharides and the oligosaccharide precursor used for N-linked glycosylation of proteins. Mutations in this gene are associated with congenital disorder of glycosylation type Iq. [provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
Variant 4-55369693-T-C is Benign according to our data. Variant chr4-55369693-T-C is described in ClinVar as [Benign]. Clinvar id is 676204.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRD5A3 | NM_024592.5 | c.698-139T>C | intron_variant | ENST00000264228.9 | |||
SRD5A3-AS1 | NR_037969.1 | n.364-2530A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRD5A3 | ENST00000264228.9 | c.698-139T>C | intron_variant | 1 | NM_024592.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.282 AC: 42454AN: 150468Hom.: 6219 Cov.: 29
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GnomAD4 exome AF: 0.292 AC: 242029AN: 829934Hom.: 36922 Cov.: 11 AF XY: 0.297 AC XY: 127017AN XY: 428126
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GnomAD4 genome AF: 0.282 AC: 42482AN: 150576Hom.: 6226 Cov.: 29 AF XY: 0.287 AC XY: 21051AN XY: 73408
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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 | Jun 16, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
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BayesDel_noAF
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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