rs11563929

Positions:

• chr7-90237531-G-T

Variant summary

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

The NM_001244944.2(STEAP2):​c.*4907G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0162 in 152,934 control chromosomes in the GnomAD database, including 154 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 0.016 (154 hom., cov: 32)
  • Exomes 𝑓: 0.012 (0 hom.)
• Consequence: STEAP2 NM_001244944.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.547

Genes affected

STEAP2 (HGNC:17885): (STEAP2 metalloreductase) This gene is a member of the STEAP family and encodes a multi-pass membrane protein that localizes to the Golgi complex, the plasma membrane, and the vesicular tubular structures in the cytosol. A highly similar protein in mouse has both ferrireductase and cupric reductase activity, and stimulates the cellular uptake of both iron and copper in vitro. Increased transcriptional expression of the human gene is associated with prostate cancer progression. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.184 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STEAP2	NM_001244944.2	c.*4907G>T		3_prime_UTR_variant	6/6	ENST00000394621.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP2	ENST00000394621.7	c.*4907G>T		3_prime_UTR_variant	6/6	1	NM_001244944.2	P1

Frequencies

GnomAD3 genomes AF: 0.0163 AC: 2470 AN: 151976 Hom.: 154 Cov.: 32

Gnomad AFR AF: 0.00268

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.0141

Gnomad FIN AF: 0.00114

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00166

Gnomad OTH AF: 0.00957

GnomAD4 exome AF: 0.0119 AC: 10 AN: 840 Hom.: 0 Cov.: 0 AF XY: 0.0114 AC XY: 5 AN XY: 440

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0463

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.214

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00348

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0163 AC: 2475 AN: 152094 Hom.: 154 Cov.: 32 AF XY: 0.0190 AC XY: 1413 AN XY: 74344

Gnomad4 AFR AF: 0.00267

Gnomad4 AMR AF: 0.0749

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.194

Gnomad4 SAS AF: 0.0139

Gnomad4 FIN AF: 0.00114

Gnomad4 NFE AF: 0.00166

Gnomad4 OTH AF: 0.00994

Alfa AF: 0.00823 Hom.: 43

Bravo AF: 0.0223

Asia WGS AF: 0.0970 AC: 333 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.055
DANN	Benign	0.32

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: rs11563929; hg19: chr7-89866845;