rs1880241

Variant names:

• chr7-22719850-A-G
• rs1880241
• ENST00000650428.1:n.46+7718T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-22719850-A-G
• chr7-22719850-A-T

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+7718T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.517 in 151,920 control chromosomes in the GnomAD database, including 21,272 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 0.52 (21272 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 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+7718T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78394 AN: 151802 Hom.: 21243 Cov.: 32

Gnomad AFR AF: 0.473

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.384

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.547

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

GnomAD4 genome AF: 0.517 AC: 78481 AN: 151920 Hom.: 21272 Cov.: 32 AF XY: 0.520 AC XY: 38639 AN XY: 74258

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.491

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.384

Gnomad4 NFE AF: 0.487

Gnomad4 OTH AF: 0.553

Alfa AF: 0.500 Hom.: 5083

Bravo AF: 0.534

Asia WGS AF: 0.818 AC: 2842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.8
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1880241; hg19: chr7-22759469;