rs2961280

Variant names:

• chr7-22600098-A-G
• rs2961280
• ENST00000442252.1:n.129-27338T>C

Your query was ambiguous. Multiple possible variants found:

• chr7-22600098-A-G
• chr7-22600098-A-T

Variant summary

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

The ENST00000442252.1(STEAP1B):​n.129-27338T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.506 in 151,980 control chromosomes in the GnomAD database, including 21,084 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 0.51 (21084 hom., cov: 31)
• Consequence: STEAP1B ENST00000442252.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.878
• Publications: 4 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.621 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.129-27338T>C		intron_variant	Intron 1 of 1	1
STEAP1B	ENST00000439708.1	c.-32+32712T>C		intron_variant	Intron 1 of 3	3		ENSP00000408954.1
STEAP1B	ENST00000650428.1	n.160-27338T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.506 AC: 76844 AN: 151862 Hom.: 21071 Cov.: 31

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.0677

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.573

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.626

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.506 AC: 76887 AN: 151980 Hom.: 21084 Cov.: 31 AF XY: 0.497 AC XY: 36930 AN XY: 74288

African (AFR) AF: 0.353 AC: 14643 AN: 41468

American (AMR) AF: 0.526 AC: 8026 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1577 AN: 3472

East Asian (EAS) AF: 0.0679 AC: 351 AN: 5172

South Asian (SAS) AF: 0.392 AC: 1890 AN: 4820

European-Finnish (FIN) AF: 0.573 AC: 6043 AN: 10546

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.626 AC: 42515 AN: 67936

Other (OTH) AF: 0.503 AC: 1061 AN: 2110

Alfa AF: 0.588 Hom.: 15799

Bravo AF: 0.495

Asia WGS AF: 0.267 AC: 930 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.0
DANN	Benign	0.42
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs2961280; hg19: chr7-22639717;