rs2067074

Variant names:

• chr7-22681324-G-C
• rs2067074
• ENST00000650428.1:n.46+46244C>G

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+46244C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.558 in 152,104 control chromosomes in the GnomAD database, including 25,701 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 0.56 (25701 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 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.46+46244C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.559 AC: 84886 AN: 151986 Hom.: 25704 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.853

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.700

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.692

Gnomad OTH AF: 0.572

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

GnomAD4 genome AF: 0.558 AC: 84904 AN: 152104 Hom.: 25701 Cov.: 32 AF XY: 0.552 AC XY: 41014 AN XY: 74366

Gnomad4 AFR AF: 0.388

Gnomad4 AMR AF: 0.484

Gnomad4 ASJ AF: 0.591

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.700

Gnomad4 NFE AF: 0.692

Gnomad4 OTH AF: 0.573

Alfa AF: 0.626 Hom.: 3871

Bravo AF: 0.537

Asia WGS AF: 0.303 AC: 1056 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2067074; hg19: chr7-22720943;