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. Variant got -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

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

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.431

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.415

Gnomad4 OTH AF: 0.409

Alfa AF: 0.401 Hom.: 16793

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7805828; hg19: chr7-22758562;