rs2056576

Variant names:

• chr7-22721583-C-T
• rs2056576
• ENST00000650428.1:n.46+5985G>A

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+5985G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 151,842 control chromosomes in the GnomAD database, including 8,860 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 0.34 (8860 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.723
• Publications: 31 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650428.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STEAP1B	ENST00000650428.1		n.46+5985G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.336 AC: 50908 AN: 151726 Hom.: 8851 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.0655

Gnomad SAS AF: 0.212

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.344

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

GnomAD4 genome AF: 0.336 AC: 50955 AN: 151842 Hom.: 8860 Cov.: 32 AF XY: 0.331 AC XY: 24552 AN XY: 74220

African (AFR) AF: 0.405 AC: 16759 AN: 41364

American (AMR) AF: 0.348 AC: 5305 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1479 AN: 3466

East Asian (EAS) AF: 0.0657 AC: 340 AN: 5176

South Asian (SAS) AF: 0.213 AC: 1026 AN: 4822

European-Finnish (FIN) AF: 0.275 AC: 2899 AN: 10536

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.324 AC: 21982 AN: 67906

Other (OTH) AF: 0.339 AC: 714 AN: 2108

Alfa AF: 0.336 Hom.: 14881

Bravo AF: 0.348

Asia WGS AF: 0.159 AC: 550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.9
DANN	Benign	0.47
PhyloP100		0.72

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2056576;

hg19: chr7-22761202;