rs1880242

Variant names:

• chr7-22719988-G-T
• rs1880242
• ENST00000650428.1:n.46+7580C>A

Variant summary

Our verdict is Benign. Variant got -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

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=-0.94).
• 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

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.581

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.520

Gnomad4 OTH AF: 0.607

Alfa AF: 0.536 Hom.: 11444

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1880242; hg19: chr7-22759607;