rs6963444

Variant names:

• chr7-22717536-A-G
• rs6963444
• ENST00000650428.1:n.46+10032T>C

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+10032T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.063 in 152,288 control chromosomes in the GnomAD database, including 605 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 0.063 (605 hom., cov: 33)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.156 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+10032T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0629 AC: 9573 AN: 152170 Hom.: 604 Cov.: 33

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0538

Gnomad ASJ AF: 0.0374

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0430

Gnomad FIN AF: 0.0217

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0212

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0630 AC: 9594 AN: 152288 Hom.: 605 Cov.: 33 AF XY: 0.0624 AC XY: 4646 AN XY: 74466

African (AFR) AF: 0.160 AC: 6628 AN: 41536

American (AMR) AF: 0.0542 AC: 829 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0374 AC: 130 AN: 3472

East Asian (EAS) AF: 0.00154 AC: 8 AN: 5188

South Asian (SAS) AF: 0.0426 AC: 206 AN: 4832

European-Finnish (FIN) AF: 0.0217 AC: 230 AN: 10622

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0212 AC: 1440 AN: 68028

Other (OTH) AF: 0.0516 AC: 109 AN: 2114

Alfa AF: 0.0549 Hom.: 82

Bravo AF: 0.0706

Asia WGS AF: 0.0310 AC: 111 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.1
DANN	Benign	0.52
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs6963444; hg19: chr7-22757155;