Genetic Variant NM_001047.4:c.90C>G (chr5-6633666-C-G) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001047.4(SRD5A1):c.90C>G(p.Arg30Arg) 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

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

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]

SRD5A1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 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_multiple_submitters_no_conflicts, 2 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 rank	MANE	Protein	UniProt
SRD5A1	NM_001047.4 link	c.90C>G	p.Arg30Arg	synonymous_variant	Exon 1 of 5	ENST00000274192.7	NP_001038.1	P18405
SRD5A1	NM_001324322.2 link	c.116C>G	p.Ala39Gly	missense_variant	Exon 1 of 4		NP_001311251.1	P18405
SRD5A1	NM_001324323.2 link	c.-632C>G		5_prime_UTR_variant	Exon 1 of 6		NP_001311252.1	P18405B7Z4D8
SRD5A1	NR_136739.2 link	n.227C>G		non_coding_transcript_exon_variant	Exon 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SRD5A1	ENST00000274192.7 link	c.90C>G	p.Arg30Arg	synonymous_variant	Exon 1 of 5	1	NM_001047.4	ENSP00000274192.5	P18405
SRD5A1	ENST00000504286.1 link	n.211C>G		non_coding_transcript_exon_variant	Exon 1 of 3	2		ENSP00000518753.1
SRD5A1	ENST00000510531.5 link	n.90C>G		non_coding_transcript_exon_variant	Exon 1 of 6	2		ENSP00000425330.1	D6RDL6
SRD5A1	ENST00000513117.1 link	n.90C>G		non_coding_transcript_exon_variant	Exon 1 of 4	2		ENSP00000421342.1	D6RG03

Frequencies

GnomAD3 genomes

AF:

0.574

AC:

87183

AN:

151970

Hom.:

25361

Cov.:

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.:

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

AF:

0.574

AC:

87258

AN:

152086

Hom.:

25380

Cov.:

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:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Sep 11, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over