chr2-31542061-A-G

Position:

• chr2-31542061-A-G

Variant summary

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

The NM_000348.4(SRD5A2):​c.282-8295T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.789 in 152,174 control chromosomes in the GnomAD database, including 48,138 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 0.79 (48138 hom., cov: 32)
• Consequence: SRD5A2 NM_000348.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SRD5A2	NM_000348.4	c.282-8295T>C		intron_variant		ENST00000622030.2	NP_000339.2
SRD5A2	XM_011533069.3	c.60-8295T>C		intron_variant			XP_011531371.1
SRD5A2	XM_011533072.3	c.27-8295T>C		intron_variant			XP_011531374.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SRD5A2	ENST00000622030.2	c.282-8295T>C		intron_variant		1	NM_000348.4	ENSP00000477587	P1
	ENST00000435713.1	n.255+14361A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.789 AC: 119953 AN: 152054 Hom.: 48075 Cov.: 32

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.758

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.789 AC: 120077 AN: 152174 Hom.: 48138 Cov.: 32 AF XY: 0.786 AC XY: 58470 AN XY: 74376

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.759

Gnomad4 ASJ AF: 0.802

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.630

Gnomad4 FIN AF: 0.750

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.795

Alfa AF: 0.824 Hom.: 11460

Bravo AF: 0.797

Asia WGS AF: 0.620 AC: 2157 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	6.9
DANN	Benign	0.58

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: rs4952197; hg19: chr2-31767131;