NM_001047.4:c.563-1606G>A

Variant names:

• chr5-6661210-G-A
• rs248797
• NM_001047.4:c.563-1606G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001047.4(SRD5A1):​c.563-1606G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,846 control chromosomes in the GnomAD database, including 21,740 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 0.53 (21740 hom., cov: 31)
• Consequence: SRD5A1 NM_001047.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 4 publications found

Genes affected

SRD5A1 (HGNC:11284): (steroid 5 alpha-reductase 1) Steroid 5-alpha-reductase (EC 1.3.99.5) catalyzes the conversion of testosterone into the more potent androgen, dihydrotestosterone (DHT). Also see SRD5A2 (MIM 607306).[supplied by OMIM, Mar 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001047.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRD5A1	NM_001047.4	MANE Select	c.563-1606G>A		intron	N/A	NP_001038.1
	SRD5A1	NM_001324322.2		c.422-1606G>A		intron	N/A	NP_001311251.1
	SRD5A1	NM_001324323.2		c.344-1606G>A		intron	N/A	NP_001311252.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRD5A1	ENST00000274192.7	TSL:1 MANE Select	c.563-1606G>A		intron	N/A	ENSP00000274192.5
	SRD5A1	ENST00000504286.2	TSL:2	n.753-1606G>A		intron	N/A	ENSP00000518753.1
	SRD5A1	ENST00000510531.6	TSL:2	n.*684-1606G>A		intron	N/A	ENSP00000425330.1

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80661 AN: 151728 Hom.: 21718 Cov.: 31

Gnomad AFR AF: 0.589

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.527

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.532 AC: 80727 AN: 151846 Hom.: 21740 Cov.: 31 AF XY: 0.529 AC XY: 39247 AN XY: 74188

African (AFR) AF: 0.588 AC: 24362 AN: 41398

American (AMR) AF: 0.572 AC: 8724 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1804 AN: 3466

East Asian (EAS) AF: 0.455 AC: 2344 AN: 5154

South Asian (SAS) AF: 0.394 AC: 1896 AN: 4812

European-Finnish (FIN) AF: 0.527 AC: 5547 AN: 10528

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34251 AN: 67928

Other (OTH) AF: 0.523 AC: 1099 AN: 2100

Alfa AF: 0.387 Hom.: 1015

Bravo AF: 0.543

Asia WGS AF: 0.455 AC: 1585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.40
DANN	Benign	0.86
PhyloP100		-1.5
Mutation Taster		=100/0	polymorphism (auto)

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: rs248797; hg19: chr5-6661323;