rs2905342

Variant names:

• chr7-22691425-C-T
• rs2905342
• ENST00000650428.1:n.46+36143G>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+36143G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 151,984 control chromosomes in the GnomAD database, including 26,020 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 0.56 (26020 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 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+36143G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.564 AC: 85586 AN: 151866 Hom.: 26022 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.591

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.563 AC: 85601 AN: 151984 Hom.: 26020 Cov.: 32 AF XY: 0.557 AC XY: 41417 AN XY: 74292

African (AFR) AF: 0.399 AC: 16527 AN: 41400

American (AMR) AF: 0.487 AC: 7433 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.591 AC: 2051 AN: 3468

East Asian (EAS) AF: 0.136 AC: 705 AN: 5178

South Asian (SAS) AF: 0.441 AC: 2126 AN: 4816

European-Finnish (FIN) AF: 0.702 AC: 7410 AN: 10560

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.694 AC: 47149 AN: 67970

Other (OTH) AF: 0.580 AC: 1223 AN: 2108

Alfa AF: 0.595 Hom.: 4199

Bravo AF: 0.543

Asia WGS AF: 0.310 AC: 1080 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.55
PhyloP100		0.015

Splicing

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

Other links and lift over

dbSNP: rs2905342; hg19: chr7-22731044;