rs7805828

Variant names:

• chr7-22718943-G-A
• rs7805828
• ENST00000650428.1:n.46+8625C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-22718943-G-A
• chr7-22718943-G-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+8625C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.389 in 151,974 control chromosomes in the GnomAD database, including 11,593 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 0.39 (11593 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.390
• Publications: 24 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.422 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+8625C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.388 AC: 58994 AN: 151856 Hom.: 11581 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.415

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.389 AC: 59047 AN: 151974 Hom.: 11593 Cov.: 32 AF XY: 0.383 AC XY: 28416 AN XY: 74272

African (AFR) AF: 0.382 AC: 15842 AN: 41424

American (AMR) AF: 0.431 AC: 6583 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.393 AC: 1362 AN: 3468

East Asian (EAS) AF: 0.238 AC: 1234 AN: 5174

South Asian (SAS) AF: 0.312 AC: 1502 AN: 4814

European-Finnish (FIN) AF: 0.283 AC: 2989 AN: 10546

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.415 AC: 28227 AN: 67960

Other (OTH) AF: 0.409 AC: 864 AN: 2112

Alfa AF: 0.402 Hom.: 21347

Bravo AF: 0.401

Asia WGS AF: 0.308 AC: 1070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.3
DANN	Benign	0.66
PhyloP100		0.39

Splicing

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

Other links and lift over

dbSNP: rs7805828; hg19: chr7-22758562;