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GeneBe

5-6633666-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

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.446
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
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
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.446 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
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
SRD5A1NM_001047.4 linkuse as main transcriptc.90C>G p.Arg30= synonymous_variant 1/5 ENST00000274192.7
SRD5A1NM_001324322.2 linkuse as main transcriptc.116C>G p.Ala39Gly missense_variant 1/4
SRD5A1NM_001324323.2 linkuse as main transcriptc.-632C>G 5_prime_UTR_variant 1/6
SRD5A1NR_136739.2 linkuse as main transcriptn.227C>G non_coding_transcript_exon_variant 1/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SRD5A1ENST00000274192.7 linkuse as main transcriptc.90C>G p.Arg30= synonymous_variant 1/51 NM_001047.4 P1
SRD5A1ENST00000504286.2 linkuse as main transcriptc.90C>G p.Arg30= synonymous_variant, NMD_transcript_variant 1/62
SRD5A1ENST00000513117.1 linkuse as main transcriptc.90C>G p.Arg30= synonymous_variant, NMD_transcript_variant 1/42
SRD5A1ENST00000510531.6 linkuse as main transcriptc.90C>G p.Arg30= synonymous_variant, NMD_transcript_variant 1/62

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.574
AC:
87183
AN:
151970
Hom.:
25361
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.645
Gnomad AMI
AF:
0.679
Gnomad AMR
AF:
0.597
Gnomad ASJ
AF:
0.541
Gnomad EAS
AF:
0.410
Gnomad SAS
AF:
0.508
Gnomad FIN
AF:
0.560
Gnomad MID
AF:
0.557
Gnomad NFE
AF:
0.545
Gnomad OTH
AF:
0.566
GnomAD3 exomes
AF:
0.547
AC:
104315
AN:
190608
Hom.:
28774
AF XY:
0.543
AC XY:
57813
AN XY:
106504
show subpopulations
Gnomad AFR exome
AF:
0.652
Gnomad AMR exome
AF:
0.622
Gnomad ASJ exome
AF:
0.544
Gnomad EAS exome
AF:
0.405
Gnomad SAS exome
AF:
0.516
Gnomad FIN exome
AF:
0.555
Gnomad NFE exome
AF:
0.542
Gnomad OTH exome
AF:
0.554
GnomAD4 exome
AF:
0.546
AC:
779586
AN:
1427056
Hom.:
214063
Cov.:
68
AF XY:
0.545
AC XY:
385981
AN XY:
708792
show subpopulations
Gnomad4 AFR exome
AF:
0.651
Gnomad4 AMR exome
AF:
0.619
Gnomad4 ASJ exome
AF:
0.542
Gnomad4 EAS exome
AF:
0.410
Gnomad4 SAS exome
AF:
0.516
Gnomad4 FIN exome
AF:
0.560
Gnomad4 NFE exome
AF:
0.547
Gnomad4 OTH exome
AF:
0.545
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.574
AC:
87258
AN:
152086
Hom.:
25380
Cov.:
35
AF XY:
0.571
AC XY:
42462
AN XY:
74372
show subpopulations
Gnomad4 AFR
AF:
0.645
Gnomad4 AMR
AF:
0.597
Gnomad4 ASJ
AF:
0.541
Gnomad4 EAS
AF:
0.410
Gnomad4 SAS
AF:
0.509
Gnomad4 FIN
AF:
0.560
Gnomad4 NFE
AF:
0.545
Gnomad4 OTH
AF:
0.566
Alfa
AF:
0.554
Hom.:
4331
Bravo
AF:
0.582
Asia WGS
AF:
0.513
AC:
1782
AN:
3468

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 submitterclinical testingGeneDxSep 11, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
Cadd
Benign
6.0
Dann
Benign
0.66

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs248793; hg19: chr5-6633779; COSMIC: COSV52952592; COSMIC: COSV52952592; API