rs2905325

Variant names:

• chr7-22673258-G-A
• rs2905325
• ENST00000650428.1:n.47-40336C>T

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.47-40336C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.874 in 152,234 control chromosomes in the GnomAD database, including 59,445 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 0.87 (59445 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.159
• Publications: 5 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 = 0.945 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.47-40336C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.874 AC: 133021 AN: 152116 Hom.: 59417 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.811

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.869

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

GnomAD4 genome AF: 0.874 AC: 133102 AN: 152234 Hom.: 59445 Cov.: 32 AF XY: 0.867 AC XY: 64539 AN XY: 74432

African (AFR) AF: 0.840 AC: 34897 AN: 41520

American (AMR) AF: 0.810 AC: 12396 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3180 AN: 3470

East Asian (EAS) AF: 0.316 AC: 1629 AN: 5160

South Asian (SAS) AF: 0.683 AC: 3294 AN: 4826

European-Finnish (FIN) AF: 0.942 AC: 9997 AN: 10610

Middle Eastern (MID) AF: 0.922 AC: 271 AN: 294

European-Non Finnish (NFE) AF: 0.951 AC: 64708 AN: 68028

Other (OTH) AF: 0.868 AC: 1836 AN: 2116

Alfa AF: 0.925 Hom.: 183216

Bravo AF: 0.865

Asia WGS AF: 0.550 AC: 1917 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	2.9
DANN	Benign	0.48
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs2905325; hg19: chr7-22712877;