rs1476482

Variant names:

• chr7-22691090-G-A
• rs1476482
• ENST00000650428.1:n.46+36478C>T

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+36478C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.803 in 152,128 control chromosomes in the GnomAD database, including 51,551 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 0.80 (51551 hom., cov: 31)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 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+36478C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122179 AN: 152010 Hom.: 51549 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.803 AC: 122203 AN: 152128 Hom.: 51551 Cov.: 31 AF XY: 0.799 AC XY: 59411 AN XY: 74376

African (AFR) AF: 0.603 AC: 24980 AN: 41448

American (AMR) AF: 0.780 AC: 11919 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.915 AC: 3172 AN: 3468

East Asian (EAS) AF: 0.307 AC: 1588 AN: 5166

South Asian (SAS) AF: 0.678 AC: 3270 AN: 4824

European-Finnish (FIN) AF: 0.939 AC: 9956 AN: 10604

Middle Eastern (MID) AF: 0.898 AC: 264 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64428 AN: 68012

Other (OTH) AF: 0.819 AC: 1732 AN: 2114

Alfa AF: 0.894 Hom.: 258953

Bravo AF: 0.783

Asia WGS AF: 0.517 AC: 1803 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.78
PhyloP100		-0.055

Splicing

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

Other links and lift over

dbSNP: rs1476482; hg19: chr7-22730709;