rs1880242

Variant names:

• chr7-22719988-G-T
• rs1880242
• ENST00000650428.1:n.46+7580C>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+7580C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,090 control chromosomes in the GnomAD database, including 28,727 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 0.60 (28727 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516
• Publications: 25 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 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+7580C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90419 AN: 151972 Hom.: 28696 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.607

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

GnomAD4 genome AF: 0.595 AC: 90512 AN: 152090 Hom.: 28727 Cov.: 32 AF XY: 0.590 AC XY: 43843 AN XY: 74316

African (AFR) AF: 0.820 AC: 34034 AN: 41506

American (AMR) AF: 0.581 AC: 8877 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2191 AN: 3472

East Asian (EAS) AF: 0.242 AC: 1251 AN: 5164

South Asian (SAS) AF: 0.456 AC: 2200 AN: 4820

European-Finnish (FIN) AF: 0.442 AC: 4661 AN: 10556

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35335 AN: 67978

Other (OTH) AF: 0.607 AC: 1278 AN: 2106

Alfa AF: 0.539 Hom.: 12830

Bravo AF: 0.620

Asia WGS AF: 0.395 AC: 1374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.8
DANN	Benign	0.40
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs1880242; hg19: chr7-22759607;