rs16877779

Variant names:

• chr5-6670536-G-A
• rs16877779
• NM_001047.4:c.*2268G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-6670536-G-A
• chr5-6670536-G-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.*2268G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0755 in 152,276 control chromosomes in the GnomAD database, including 499 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 0.076 (499 hom., cov: 33)
  • Exomes 𝑓: 0.031 (0 hom.)
• Consequence: SRD5A1 NM_001047.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.817
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.185 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.*2268G>A		3_prime_UTR	Exon 5 of 5	NP_001038.1
	SRD5A1	NR_136739.2		n.3375G>A		non_coding_transcript_exon	Exon 6 of 6
	SRD5A1	NM_001324322.2		c.*2268G>A		3_prime_UTR	Exon 4 of 4	NP_001311251.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SRD5A1	ENST00000274192.7	TSL:1 MANE Select	c.*2268G>A		3_prime_UTR	Exon 5 of 5	ENSP00000274192.5
	SRD5A1	ENST00000504286.2	TSL:2	n.*2473G>A		non_coding_transcript_exon	Exon 6 of 6	ENSP00000518753.1
	SRD5A1	ENST00000504286.2	TSL:2	n.*2473G>A		3_prime_UTR	Exon 6 of 6	ENSP00000518753.1

Frequencies

GnomAD3 genomes AF: 0.0756 AC: 11503 AN: 152126 Hom.: 502 Cov.: 33

Gnomad AFR AF: 0.0342

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.0959

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0595

Gnomad FIN AF: 0.0845

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0923

Gnomad OTH AF: 0.0807

GnomAD4 exome AF: 0.0313 AC: 1 AN: 32 Hom.: 0 Cov.: 0 AF XY: 0.0357 AC XY: 1 AN XY: 28

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 28

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.0755 AC: 11499 AN: 152244 Hom.: 499 Cov.: 33 AF XY: 0.0756 AC XY: 5624 AN XY: 74428

African (AFR) AF: 0.0341 AC: 1419 AN: 41564

American (AMR) AF: 0.0677 AC: 1034 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0959 AC: 333 AN: 3472

East Asian (EAS) AF: 0.195 AC: 1007 AN: 5176

South Asian (SAS) AF: 0.0595 AC: 287 AN: 4820

European-Finnish (FIN) AF: 0.0845 AC: 894 AN: 10582

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0923 AC: 6279 AN: 68024

Other (OTH) AF: 0.0841 AC: 178 AN: 2116

Alfa AF: 0.0824 Hom.: 790

Bravo AF: 0.0728

Asia WGS AF: 0.0970 AC: 339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.97
DANN	Benign	0.37
PhyloP100		-0.82

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: rs16877779; hg19: chr5-6670649;