rs2961298

Variant names:

• chr7-22668472-T-G
• rs2961298
• ENST00000650428.1:n.47-35550A>C

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.47-35550A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 151,972 control chromosomes in the GnomAD database, including 25,215 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 0.54 (25215 hom., cov: 31)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.39
• Publications: 6 publications found

Genes affected

STEAP1B (HGNC:41907): (STEAP family member 1B) Predicted to be integral component of membrane. Predicted to be active in endosome and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000650428.1	n.47-35550A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82603 AN: 151854 Hom.: 25216 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.544 AC: 82620 AN: 151972 Hom.: 25215 Cov.: 31 AF XY: 0.539 AC XY: 40004 AN XY: 74280

African (AFR) AF: 0.326 AC: 13520 AN: 41438

American (AMR) AF: 0.488 AC: 7458 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.623 AC: 2159 AN: 3466

East Asian (EAS) AF: 0.0738 AC: 381 AN: 5166

South Asian (SAS) AF: 0.429 AC: 2064 AN: 4810

European-Finnish (FIN) AF: 0.707 AC: 7461 AN: 10554

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47511 AN: 67948

Other (OTH) AF: 0.559 AC: 1178 AN: 2108

Alfa AF: 0.629 Hom.: 20413

Bravo AF: 0.516

Asia WGS AF: 0.274 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.15
DANN	Benign	0.59
PhyloP100		-3.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2961298; hg19: chr7-22708091;