5-6661853-C-T

Position:

• chr5-6661853-C-T

Variant summary

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

The NM_001047.4(SRD5A1):​c.563-963C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,996 control chromosomes in the GnomAD database, including 8,150 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 0.32 (8150 hom., cov: 32)
• Consequence: SRD5A1 NM_001047.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0410

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SRD5A1	NM_001047.4	c.563-963C>T		intron_variant		ENST00000274192.7	NP_001038.1
SRD5A1	NM_001324322.2	c.422-963C>T		intron_variant			NP_001311251.1
SRD5A1	NM_001324323.2	c.344-963C>T		intron_variant			NP_001311252.1
SRD5A1	NR_136739.2	n.890-963C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SRD5A1	ENST00000274192.7	c.563-963C>T		intron_variant		1	NM_001047.4	ENSP00000274192	P1
SRD5A1	ENST00000504286.2	c.753-963C>T		intron_variant, NMD_transcript_variant		2		ENSP00000518753
SRD5A1	ENST00000510531.6	c.*684-963C>T		intron_variant, NMD_transcript_variant		2		ENSP00000425330
SRD5A1	ENST00000513117.1	c.396-963C>T		intron_variant, NMD_transcript_variant		2		ENSP00000421342

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48540 AN: 151878 Hom.: 8151 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.471

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.448

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.374

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.320 AC: 48570 AN: 151996 Hom.: 8150 Cov.: 32 AF XY: 0.313 AC XY: 23254 AN XY: 74296

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.448

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.374

Gnomad4 OTH AF: 0.354

Alfa AF: 0.373 Hom.: 10272

Bravo AF: 0.323

Asia WGS AF: 0.201 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.68
DANN	Benign	0.71

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

Publications

LitVar

Other links and lift over

dbSNP: rs6884552; hg19: chr5-6661966;