rs2073990

Variant names:

• chr7-22690342-G-A
• rs2073990
• ENST00000915078.1:c.-145+16342C>T

Variant summary

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

The ENST00000915078.1(STEAP1B):​c.-145+16342C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.848 in 152,202 control chromosomes in the GnomAD database, including 56,141 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 0.85 (56141 hom., cov: 33)
• Consequence: STEAP1B ENST00000915078.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0160
• Publications: 1 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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000915078.1. 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	ENST00000915078.1		c.-145+16342C>T		intron	N/A	ENSP00000585137.1
	STEAP1B	ENST00000915079.1		c.-145+15285C>T		intron	N/A	ENSP00000585138.1
	STEAP1B	ENST00000915080.1		c.-104+15285C>T		intron	N/A	ENSP00000585139.1

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128962 AN: 152084 Hom.: 56131 Cov.: 33

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.797

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.948

Gnomad OTH AF: 0.853

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

GnomAD4 genome AF: 0.848 AC: 129013 AN: 152202 Hom.: 56141 Cov.: 33 AF XY: 0.842 AC XY: 62638 AN XY: 74416

African (AFR) AF: 0.754 AC: 31273 AN: 41494

American (AMR) AF: 0.796 AC: 12172 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.916 AC: 3181 AN: 3472

East Asian (EAS) AF: 0.313 AC: 1617 AN: 5158

South Asian (SAS) AF: 0.687 AC: 3313 AN: 4822

European-Finnish (FIN) AF: 0.939 AC: 9969 AN: 10622

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.948 AC: 64524 AN: 68028

Other (OTH) AF: 0.851 AC: 1800 AN: 2114

Alfa AF: 0.874 Hom.: 8657

Bravo AF: 0.835

Asia WGS AF: 0.544 AC: 1895 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.30
DANN	Benign	0.34
PhyloP100		0.016

Splicing

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

Other links and lift over

dbSNP: rs2073990; hg19: chr7-22729961;