7-90213316-G-A

Variant names:

• chr7-90213316-G-A
• rs194506
• NM_001244944.2:c.-147+1271G>A

Variant summary

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

The NM_001244944.2(STEAP2):​c.-147+1271G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 152,294 control chromosomes in the GnomAD database, including 61,980 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 0.90 (61980 hom., cov: 33)
• Consequence: STEAP2 NM_001244944.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0900
• Publications: 3 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STEAP2	NM_001244944.2	c.-147+1271G>A		intron_variant	Intron 1 of 5	ENST00000394621.7	NP_001231873.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STEAP2	ENST00000394621.7	c.-147+1271G>A		intron_variant	Intron 1 of 5	1	NM_001244944.2	ENSP00000378119.2

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136971 AN: 152176 Hom.: 61923 Cov.: 33

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.855

Gnomad AMR AF: 0.889

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.948

Gnomad FIN AF: 0.898

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.900 AC: 137088 AN: 152294 Hom.: 61980 Cov.: 33 AF XY: 0.904 AC XY: 67290 AN XY: 74458

African (AFR) AF: 0.971 AC: 40359 AN: 41584

American (AMR) AF: 0.889 AC: 13600 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2951 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5182 AN: 5188

South Asian (SAS) AF: 0.948 AC: 4571 AN: 4822

European-Finnish (FIN) AF: 0.898 AC: 9519 AN: 10598

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57981 AN: 68018

Other (OTH) AF: 0.889 AC: 1879 AN: 2114

Alfa AF: 0.866 Hom.: 2791

Bravo AF: 0.900

Asia WGS AF: 0.967 AC: 3362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	8.2
DANN	Benign	0.58
PhyloP100		0.090
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs194506; hg19: chr7-89842630;