rs2961283

Variant names:

• chr7-22600879-G-A
• rs2961283
• ENST00000442252.1:n.129-28119C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000442252.1(STEAP1B):​n.129-28119C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 152,068 control chromosomes in the GnomAD database, including 20,141 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 0.49 (20141 hom., cov: 32)
• Consequence: STEAP1B ENST00000442252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697
• Publications: 5 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]

STEAP1B-AS1 (HGNC:56137): (STEAP1B antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 = 0.619 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	ENST00000442252.1	n.129-28119C>T		intron_variant	Intron 1 of 1	1
STEAP1B	ENST00000439708.1	c.-32+31931C>T		intron_variant	Intron 1 of 3	3		ENSP00000408954.1
STEAP1B	ENST00000650428.1	n.160-28119C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.491 AC: 74661 AN: 151950 Hom.: 20138 Cov.: 32

Gnomad AFR AF: 0.338

Gnomad AMI AF: 0.713

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.452

Gnomad EAS AF: 0.0518

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.624

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.491 AC: 74683 AN: 152068 Hom.: 20141 Cov.: 32 AF XY: 0.482 AC XY: 35789 AN XY: 74320

African (AFR) AF: 0.337 AC: 13983 AN: 41480

American (AMR) AF: 0.441 AC: 6733 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.452 AC: 1568 AN: 3470

East Asian (EAS) AF: 0.0519 AC: 268 AN: 5166

South Asian (SAS) AF: 0.390 AC: 1882 AN: 4822

European-Finnish (FIN) AF: 0.572 AC: 6043 AN: 10568

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.624 AC: 42409 AN: 67978

Other (OTH) AF: 0.482 AC: 1015 AN: 2106

Alfa AF: 0.573 Hom.: 14145

Bravo AF: 0.471

Asia WGS AF: 0.255 AC: 887 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	1.6
DANN	Benign	0.53
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs2961283; hg19: chr7-22640498;