chr5-6666809-G-A

Variant names:

• chr5-6666809-G-A
• rs3797179
• NM_001047.4:c.714-1393G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001047.4(SRD5A1):​c.714-1393G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 152,128 control chromosomes in the GnomAD database, including 1,144 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1144 hom., cov: 32)
• Consequence: SRD5A1 NM_001047.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.997
• Publications: 10 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRD5A1	NM_001047.4	c.714-1393G>A		intron_variant	Intron 4 of 4	ENST00000274192.7	NP_001038.1
SRD5A1	NM_001324322.2	c.573-1393G>A		intron_variant	Intron 3 of 3		NP_001311251.1
SRD5A1	NM_001324323.2	c.495-1393G>A		intron_variant	Intron 5 of 5		NP_001311252.1
SRD5A1	NR_136739.2	n.1041-1393G>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRD5A1	ENST00000274192.7	c.714-1393G>A		intron_variant	Intron 4 of 4	1	NM_001047.4	ENSP00000274192.5
SRD5A1	ENST00000504286.2	n.*139-1393G>A		intron_variant	Intron 5 of 5	2		ENSP00000518753.1
SRD5A1	ENST00000510531.6	n.*835-1393G>A		intron_variant	Intron 5 of 5	2		ENSP00000425330.1
SRD5A1	ENST00000513117.1	n.*139-1393G>A		intron_variant	Intron 3 of 3	2		ENSP00000421342.1

Frequencies

GnomAD3 genomes AF: 0.118 AC: 17877 AN: 152010 Hom.: 1148 Cov.: 32

Gnomad AFR AF: 0.0708

Gnomad AMI AF: 0.119

Gnomad AMR AF: 0.0930

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0852

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.115

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.126

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.118 AC: 17879 AN: 152128 Hom.: 1144 Cov.: 32 AF XY: 0.118 AC XY: 8740 AN XY: 74352

African (AFR) AF: 0.0707 AC: 2934 AN: 41518

American (AMR) AF: 0.0928 AC: 1419 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.137 AC: 474 AN: 3470

East Asian (EAS) AF: 0.195 AC: 999 AN: 5136

South Asian (SAS) AF: 0.0857 AC: 412 AN: 4810

European-Finnish (FIN) AF: 0.150 AC: 1584 AN: 10578

Middle Eastern (MID) AF: 0.110 AC: 32 AN: 292

European-Non Finnish (NFE) AF: 0.142 AC: 9644 AN: 68004

Other (OTH) AF: 0.129 AC: 273 AN: 2114

Alfa AF: 0.133 Hom.: 2998

Bravo AF: 0.111

Asia WGS AF: 0.108 AC: 375 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.69
PhyloP100		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3797179; hg19: chr5-6666922;