rs559555

Positions:

• chr2-31585905-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_011533072.3(SRD5A2):​c.27-52139A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 151,954 control chromosomes in the GnomAD database, including 22,344 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 0.54 (22344 hom., cov: 31)
• Consequence: SRD5A2 XM_011533072.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.99

Genes affected

SRD5A2 (HGNC:11285): (steroid 5 alpha-reductase 2) This gene encodes a microsomal protein expressed at high levels in androgen-sensitive tissues such as the prostate. The encoded protein is active at acidic pH and is sensitive to the 4-azasteroid inhibitor finasteride. Deficiencies in this gene can result in male pseudohermaphroditism, specifically pseudovaginal perineoscrotal hypospadias (PPSH). [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SRD5A2	XM_011533072.3	c.27-52139A>T		intron_variant			XP_011531374.1
		n.31585905T>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.540 AC: 82034 AN: 151834 Hom.: 22331 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.548

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.540 AC: 82082 AN: 151954 Hom.: 22344 Cov.: 31 AF XY: 0.542 AC XY: 40286 AN XY: 74268

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.458

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.541

Alfa AF: 0.559 Hom.: 2946

Bravo AF: 0.534

Asia WGS AF: 0.420 AC: 1463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.10
DANN	Benign	0.14

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs559555; hg19: chr2-31810974;