2-31525043-TAAA-TAAAA

Variant names:

• chr2-31525043-T-TA
• rs74702388
• NM_000348.4:c.*1152dupT

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_000348.4(SRD5A2):​c.*1152dupT variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.019 (26 hom., cov: 32)
  • Exomes 𝑓: 0.37 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: SRD5A2 NM_000348.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 0 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: Orphanet, Labcorp Genetics (formerly Invitae), PanelApp Australia

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000348.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRD5A2	NM_000348.4	MANE Select	c.*1152dupT		3_prime_UTR	Exon 5 of 5	NP_000339.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRD5A2	ENST00000622030.2	TSL:1 MANE Select	c.*1152dupT		3_prime_UTR	Exon 5 of 5	ENSP00000477587.1	P31213
	SRD5A2	ENST00000882642.1		c.*1152dupT		3_prime_UTR	Exon 6 of 6	ENSP00000552701.1
	SRD5A2	ENST00000882643.1		c.*1152dupT		3_prime_UTR	Exon 4 of 4	ENSP00000552702.1

Frequencies

GnomAD3 genomes AF: 0.0192 AC: 2708 AN: 140766 Hom.: 26 Cov.: 32

Gnomad AFR AF: 0.0198

Gnomad AMI AF: 0.0426

Gnomad AMR AF: 0.0153

Gnomad ASJ AF: 0.00879

Gnomad EAS AF: 0.00344

Gnomad SAS AF: 0.00540

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.00671

Gnomad NFE AF: 0.0187

Gnomad OTH AF: 0.0205

GnomAD4 exome AF: 0.371 AC: 16522 AN: 44474 Hom.: 1 Cov.: 0 AF XY: 0.372 AC XY: 7673 AN XY: 20618

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.350 AC: 713 AN: 2038

American (AMR) AF: 0.343 AC: 453 AN: 1320

Ashkenazi Jewish (ASJ) AF: 0.384 AC: 1085 AN: 2828

East Asian (EAS) AF: 0.390 AC: 2550 AN: 6544

South Asian (SAS) AF: 0.341 AC: 124 AN: 364

European-Finnish (FIN) AF: 0.400 AC: 16 AN: 40

Middle Eastern (MID) AF: 0.349 AC: 99 AN: 284

European-Non Finnish (NFE) AF: 0.370 AC: 10112 AN: 27312

Other (OTH) AF: 0.366 AC: 1370 AN: 3744

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0193 AC: 2723 AN: 140812 Hom.: 26 Cov.: 32 AF XY: 0.0190 AC XY: 1297 AN XY: 68192

African (AFR) AF: 0.0200 AC: 770 AN: 38586

American (AMR) AF: 0.0155 AC: 218 AN: 14106

Ashkenazi Jewish (ASJ) AF: 0.00879 AC: 29 AN: 3298

East Asian (EAS) AF: 0.00345 AC: 17 AN: 4932

South Asian (SAS) AF: 0.00564 AC: 25 AN: 4432

European-Finnish (FIN) AF: 0.0458 AC: 384 AN: 8380

Middle Eastern (MID) AF: 0.00735 AC: 2 AN: 272

European-Non Finnish (NFE) AF: 0.0187 AC: 1198 AN: 64002

Other (OTH) AF: 0.0220 AC: 42 AN: 1912

Alfa AF: 0.00617 Hom.: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.41

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: rs74702388; hg19: chr2-31750113;