rs1880243

Variant names:

• chr7-22720036-C-A
• rs1880243
• ENST00000650428.1:n.46+7532G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650428.1(STEAP1B):​n.46+7532G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,072 control chromosomes in the GnomAD database, including 2,613 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 0.18 (2613 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.225 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+7532G>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27791 AN: 151954 Hom.: 2610 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.231

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0669

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.183 AC: 27820 AN: 152072 Hom.: 2613 Cov.: 32 AF XY: 0.180 AC XY: 13399 AN XY: 74332

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.231

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.0671

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.198

Gnomad4 OTH AF: 0.170

Alfa AF: 0.191 Hom.: 605

Bravo AF: 0.187

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.85
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1880243; hg19: chr7-22759655;