5-6657890-T-C

Variant names:

• chr5-6657890-T-C
• rs10060745
• NM_001047.4:c.562+1711T>C

Variant summary

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

The NM_001047.4(SRD5A1):​c.562+1711T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,070 control chromosomes in the GnomAD database, including 9,304 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 0.35 (9304 hom., cov: 33)
• Consequence: SRD5A1 NM_001047.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 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.562+1711T>C		intron	N/A	NP_001038.1
	SRD5A1	NM_001324322.2		c.421+1711T>C		intron	N/A	NP_001311251.1
	SRD5A1	NM_001324323.2		c.343+1711T>C		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.562+1711T>C		intron	N/A	ENSP00000274192.5
	SRD5A1	ENST00000854432.1		c.712+1711T>C		intron	N/A	ENSP00000524491.1
	SRD5A1	ENST00000854431.1		c.752+1711T>C		intron	N/A	ENSP00000524490.1

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52462 AN: 151952 Hom.: 9294 Cov.: 33

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.307

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.345 AC: 52512 AN: 152070 Hom.: 9304 Cov.: 33 AF XY: 0.339 AC XY: 25194 AN XY: 74308

African (AFR) AF: 0.329 AC: 13654 AN: 41476

American (AMR) AF: 0.354 AC: 5414 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1576 AN: 3472

East Asian (EAS) AF: 0.161 AC: 831 AN: 5172

South Asian (SAS) AF: 0.217 AC: 1045 AN: 4820

European-Finnish (FIN) AF: 0.307 AC: 3239 AN: 10536

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.374 AC: 25419 AN: 67992

Other (OTH) AF: 0.369 AC: 779 AN: 2112

Alfa AF: 0.336 Hom.: 1124

Bravo AF: 0.352

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.53
PhyloP100		-0.17
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: rs10060745; hg19: chr5-6658003;