2-31583901-T-C

Variant summary

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

The XM_011533072.3(SRD5A2):c.27-50135A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.685 in 151,688 control chromosomes in the GnomAD database, including 35,813 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 0.69 (35813 hom., cov: 29)
• Consequence: SRD5A2 XM_011533072.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33

Genes affected

SRD5A2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SRD5A2	XM_011533072.3	c.27-50135A>G		intron_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.686 AC: 103909 AN: 151566 Hom.: 35799 Cov.: 29

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.670

Gnomad ASJ AF: 0.754

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.690

Gnomad MID AF: 0.710

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.685 AC: 103967 AN: 151688 Hom.: 35813 Cov.: 29 AF XY: 0.685 AC XY: 50732 AN XY: 74104

Gnomad4 AFR AF: 0.690

Gnomad4 AMR AF: 0.670

Gnomad4 ASJ AF: 0.754

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.690

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.695

Alfa AF: 0.693 Hom.: 4560

Bravo AF: 0.682

Asia WGS AF: 0.523 AC: 1820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.32
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs676033; hg19: chr2-31808970;