rs2067074

Variant names:

• chr7-22681324-G-C
• rs2067074
• ENST00000915078.1:c.-145+25360C>G

Variant summary

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

The ENST00000915078.1(STEAP1B):​c.-145+25360C>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 ENST00000915078.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.844
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000915078.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STEAP1B	ENST00000915078.1		c.-145+25360C>G		intron	N/A	ENSP00000585137.1
	STEAP1B	ENST00000915079.1		c.-145+24303C>G		intron	N/A	ENSP00000585138.1
	STEAP1B	ENST00000915080.1		c.-104+24303C>G		intron	N/A	ENSP00000585139.1

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

African (AFR) AF: 0.388 AC: 16093 AN: 41454

American (AMR) AF: 0.484 AC: 7403 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2052 AN: 3470

East Asian (EAS) AF: 0.130 AC: 673 AN: 5180

South Asian (SAS) AF: 0.426 AC: 2051 AN: 4810

European-Finnish (FIN) AF: 0.700 AC: 7410 AN: 10586

Middle Eastern (MID) AF: 0.616 AC: 180 AN: 292

European-Non Finnish (NFE) AF: 0.692 AC: 47056 AN: 68000

Other (OTH) AF: 0.573 AC: 1208 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.36
DANN	Benign	0.71
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs2067074; hg19: chr7-22720943;