rs2961298

chr7-22668472-T-G

Variant summary

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

The ENST00000650428.1(STEAP1B):n.47-35550A>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.544 in 151,972 control chromosomes in the GnomAD database, including 25,215 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 0.54 (25215 hom., cov: 31)
• Consequence: STEAP1B ENST00000650428.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.39

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 (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP1B	ENST00000650428.1	n.47-35550A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.544 AC: 82603 AN: 151854 Hom.: 25216 Cov.: 31

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.623

Gnomad EAS AF: 0.0742

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.707

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.544 AC: 82620 AN: 151972 Hom.: 25215 Cov.: 31 AF XY: 0.539 AC XY: 40004 AN XY: 74280

Gnomad4 AFR AF: 0.326

Gnomad4 AMR AF: 0.488

Gnomad4 ASJ AF: 0.623

Gnomad4 EAS AF: 0.0738

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.707

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.559

Alfa AF: 0.626 Hom.: 13571

Bravo AF: 0.516

Asia WGS AF: 0.274 AC: 955 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.15
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2961298; hg19: chr7-22708091;