chr7-22721094-A-T

Variant names:

• chr7-22721094-A-T
• rs4719714
• ENST00000650428.1:n.46+6474T>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+6474T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,114 control chromosomes in the GnomAD database, including 3,352 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 0.21 (3352 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.283
• Publications: 26 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.218 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+6474T>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31806 AN: 151996 Hom.: 3347 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.179

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.215

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.209 AC: 31824 AN: 152114 Hom.: 3352 Cov.: 32 AF XY: 0.208 AC XY: 15441 AN XY: 74368

African (AFR) AF: 0.209 AC: 8677 AN: 41468

American (AMR) AF: 0.203 AC: 3106 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.179 AC: 621 AN: 3470

East Asian (EAS) AF: 0.174 AC: 902 AN: 5178

South Asian (SAS) AF: 0.214 AC: 1031 AN: 4820

European-Finnish (FIN) AF: 0.154 AC: 1627 AN: 10594

Middle Eastern (MID) AF: 0.279 AC: 81 AN: 290

European-Non Finnish (NFE) AF: 0.221 AC: 15022 AN: 67982

Other (OTH) AF: 0.238 AC: 503 AN: 2110

Alfa AF: 0.203 Hom.: 381

Bravo AF: 0.214

Asia WGS AF: 0.209 AC: 725 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.2
DANN	Benign	0.77
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs4719714; hg19: chr7-22760713;