7-22717884-C-T

Variant names:

• chr7-22717884-C-T
• rs1546762
• ENST00000650428.1:n.46+9684G>A

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+9684G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 152,020 control chromosomes in the GnomAD database, including 27,858 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 0.59 (27858 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650428.1. 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	ENST00000650428.1		n.46+9684G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89307 AN: 151902 Hom.: 27836 Cov.: 32

Gnomad AFR AF: 0.797

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.440

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.588 AC: 89390 AN: 152020 Hom.: 27858 Cov.: 32 AF XY: 0.583 AC XY: 43312 AN XY: 74296

African (AFR) AF: 0.796 AC: 33021 AN: 41468

American (AMR) AF: 0.580 AC: 8860 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2187 AN: 3464

East Asian (EAS) AF: 0.242 AC: 1254 AN: 5176

South Asian (SAS) AF: 0.456 AC: 2199 AN: 4818

European-Finnish (FIN) AF: 0.440 AC: 4638 AN: 10532

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35273 AN: 67960

Other (OTH) AF: 0.603 AC: 1273 AN: 2110

Alfa AF: 0.570 Hom.: 4787

Bravo AF: 0.612

Asia WGS AF: 0.394 AC: 1368 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.78
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1546762; hg19: chr7-22757503;