rs2961298

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.0738

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.559

Alfa AF: 0.626 Hom.: 13571

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2961298; hg19: chr7-22708091;