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GeneBe

5-6656094-A-G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7

The NM_001047.4(SRD5A1):c.477A>G(p.Leu159=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000528 in 1,613,938 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0024 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00034 ( 3 hom. )

Consequence

SRD5A1
NM_001047.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.480
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 -7 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=-0.84).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-6656094-A-G is Benign according to our data. Variant chr5-6656094-A-G is described in ClinVar as [Benign]. Clinvar id is 791132.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=-0.48 with no splicing effect.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SRD5A1NM_001047.4 linkuse as main transcriptc.477A>G p.Leu159= synonymous_variant 3/5 ENST00000274192.7
SRD5A1NM_001324322.2 linkuse as main transcriptc.336A>G p.Leu112= synonymous_variant 2/4
SRD5A1NM_001324323.2 linkuse as main transcriptc.258A>G p.Leu86= synonymous_variant 4/6
SRD5A1NR_136739.2 linkuse as main transcriptn.804A>G non_coding_transcript_exon_variant 4/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SRD5A1ENST00000274192.7 linkuse as main transcriptc.477A>G p.Leu159= synonymous_variant 3/51 NM_001047.4 P1
SRD5A1ENST00000504286.2 linkuse as main transcriptc.667A>G p.Asn223Asp missense_variant, NMD_transcript_variant 4/62
SRD5A1ENST00000513117.1 linkuse as main transcriptc.310A>G p.Asn104Asp missense_variant, NMD_transcript_variant 2/42
SRD5A1ENST00000510531.6 linkuse as main transcriptc.*598A>G 3_prime_UTR_variant, NMD_transcript_variant 4/62

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00238
AC:
362
AN:
152192
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00789
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00144
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00478
GnomAD3 exomes
AF:
0.000705
AC:
177
AN:
251172
Hom.:
0
AF XY:
0.000508
AC XY:
69
AN XY:
135778
show subpopulations
Gnomad AFR exome
AF:
0.00819
Gnomad AMR exome
AF:
0.000638
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000167
Gnomad OTH exome
AF:
0.000491
GnomAD4 exome
AF:
0.000336
AC:
491
AN:
1461628
Hom.:
3
Cov.:
29
AF XY:
0.000290
AC XY:
211
AN XY:
727112
show subpopulations
Gnomad4 AFR exome
AF:
0.00917
Gnomad4 AMR exome
AF:
0.000851
Gnomad4 ASJ exome
AF:
0.0000383
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000809
Gnomad4 OTH exome
AF:
0.000828
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.00237
AC:
361
AN:
152310
Hom.:
0
Cov.:
33
AF XY:
0.00239
AC XY:
178
AN XY:
74468
show subpopulations
Gnomad4 AFR
AF:
0.00784
Gnomad4 AMR
AF:
0.00144
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00473
Alfa
AF:
0.00144
Hom.:
0
Asia WGS
AF:
0.000289
AC:
1
AN:
3478
EpiCase
AF:
0.000327
EpiControl
AF:
0.000356

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 testingInvitaeMay 03, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.84
Cadd
Benign
0.42
Dann
Benign
0.91

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: rs8192208; hg19: chr5-6656207; API