rs12470143

chr2-31538488-C-T

Variant summary

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

The NM_000348.4(SRD5A2):c.282-4722G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.417 in 151,954 control chromosomes in the GnomAD database, including 13,663 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 0.42 (13663 hom., cov: 32)
• Consequence: SRD5A2 NM_000348.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRD5A2	NM_000348.4	c.282-4722G>A		intron_variant		ENST00000622030.2
SRD5A2	XM_011533069.3	c.60-4722G>A		intron_variant
SRD5A2	XM_011533072.3	c.27-4722G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SRD5A2	ENST00000622030.2	c.282-4722G>A		intron_variant		1	NM_000348.4	P1
	ENST00000435713.1	n.255+10788C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63312 AN: 151836 Hom.: 13664 Cov.: 32

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.353

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.414

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

GnomAD4 genome AF: 0.417 AC: 63328 AN: 151954 Hom.: 13663 Cov.: 32 AF XY: 0.419 AC XY: 31116 AN XY: 74274

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.353

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.410

Alfa AF: 0.453 Hom.: 32031

Bravo AF: 0.410

Asia WGS AF: 0.305 AC: 1062 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.88
Dann	Benign	0.74

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

Other links and lift over

dbSNP: rs12470143; hg19: chr2-31763558;