2-31578786-GT-GTT

Variant names:

• chr2-31578786-G-GT
• rs28382999
• NM_000348.4:c.281+1833dupA

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The NM_000348.4(SRD5A2):​c.281+1833dupA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 151,192 control chromosomes in the GnomAD database, including 1,403 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.13 (1403 hom., cov: 30)
• Consequence: SRD5A2 NM_000348.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.257
• Publications: 1 publications found

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]

SRD5A2 Gene-Disease associations (from GenCC):

• 46,XY disorder of sex development due to 5-alpha-reductase 2 deficiency

  Inheritance: AR Classification: STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SRD5A2	NM_000348.4	c.281+1833dupA		intron_variant	Intron 1 of 4	ENST00000622030.2	NP_000339.2
SRD5A2	XM_011533072.3	c.27-45021dupA		intron_variant	Intron 3 of 6		XP_011531374.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SRD5A2	ENST00000622030.2	c.281+1833_281+1834insA		intron_variant	Intron 1 of 4	1	NM_000348.4	ENSP00000477587.1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19497 AN: 151076 Hom.: 1400 Cov.: 30

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0808

Gnomad AMR AF: 0.0942

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.0992

Gnomad FIN AF: 0.0991

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.105

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.129 AC: 19519 AN: 151192 Hom.: 1403 Cov.: 30 AF XY: 0.129 AC XY: 9491 AN XY: 73832

African (AFR) AF: 0.184 AC: 7594 AN: 41182

American (AMR) AF: 0.0941 AC: 1426 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 928 AN: 3466

East Asian (EAS) AF: 0.106 AC: 543 AN: 5142

South Asian (SAS) AF: 0.0997 AC: 477 AN: 4782

European-Finnish (FIN) AF: 0.0991 AC: 1032 AN: 10416

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.105 AC: 7111 AN: 67768

Other (OTH) AF: 0.135 AC: 281 AN: 2088

Alfa AF: 0.0219 Hom.: 11

Asia WGS AF: 0.102 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.26

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: rs28382999; hg19: chr2-31803856;