rs11563929

Variant names:

• chr7-90237531-G-T
• rs11563929
• NM_001244944.2:c.*4907G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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]

LOC107986819 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001244944.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STEAP2	NM_001244944.2	MANE Select	c.*4907G>T		3_prime_UTR	Exon 6 of 6	NP_001231873.1	Q8NFT2-1
	STEAP2	NM_001040665.2		c.*4907G>T		3_prime_UTR	Exon 6 of 6	NP_001035755.1	Q8NFT2-1
	STEAP2	NM_152999.4		c.*4907G>T		3_prime_UTR	Exon 5 of 5	NP_694544.2	Q8NFT2-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STEAP2	ENST00000394621.7	TSL:1 MANE Select	c.*4907G>T		3_prime_UTR	Exon 6 of 6	ENSP00000378119.2	Q8NFT2-1
	STEAP2	ENST00000287908.7	TSL:1	c.*4907G>T		3_prime_UTR	Exon 5 of 5	ENSP00000287908.3	Q8NFT2-1
	STEAP2	ENST00000394622.6	TSL:1	c.*4907G>T		3_prime_UTR	Exon 6 of 6	ENSP00000378120.2	Q8NFT2-1

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

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AF: 0.0463 AC: 5 AN: 108

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 12

East Asian (EAS) AF: 0.214 AC: 3 AN: 14

South Asian (SAS) AF: 0.00 AC: 0 AN: 50

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 46

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00348 AC: 2 AN: 574

Other (OTH) AF: 0.00 AC: 0 AN: 28

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

African (AFR) AF: 0.00267 AC: 111 AN: 41502

American (AMR) AF: 0.0749 AC: 1144 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3472

East Asian (EAS) AF: 0.194 AC: 1002 AN: 5160

South Asian (SAS) AF: 0.0139 AC: 67 AN: 4812

European-Finnish (FIN) AF: 0.00114 AC: 12 AN: 10558

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.00166 AC: 113 AN: 67992

Other (OTH) AF: 0.00994 AC: 21 AN: 2112

Alfa AF: 0.00787 Hom.: 52

Bravo AF: 0.0223

Asia WGS AF: 0.0970 AC: 333 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.055
DANN	Benign	0.32
PhyloP100		-0.55
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: rs11563929; hg19: chr7-89866845;