chr7-22693220-G-A

Variant names:

• chr7-22693220-G-A
• rs2097677
• ENST00000915078.1:c.-145+13464C>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+13464C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 151,614 control chromosomes in the GnomAD database, including 4,445 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 0.24 (4445 hom., cov: 30)
• Consequence: STEAP1B ENST00000915078.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94
• Publications: 30 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 (AMR) allele frequency at 95% confidence interval = 0.286 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+13464C>T		intron	N/A	ENSP00000585137.1
	STEAP1B	ENST00000915079.1		c.-145+12407C>T		intron	N/A	ENSP00000585138.1
	STEAP1B	ENST00000915080.1		c.-104+12407C>T		intron	N/A	ENSP00000585139.1

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36309 AN: 151494 Hom.: 4442 Cov.: 30

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.170

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.287

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.240 AC: 36316 AN: 151614 Hom.: 4445 Cov.: 30 AF XY: 0.241 AC XY: 17821 AN XY: 74098

African (AFR) AF: 0.203 AC: 8385 AN: 41308

American (AMR) AF: 0.293 AC: 4464 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1118 AN: 3468

East Asian (EAS) AF: 0.171 AC: 877 AN: 5140

South Asian (SAS) AF: 0.236 AC: 1130 AN: 4798

European-Finnish (FIN) AF: 0.237 AC: 2491 AN: 10496

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17168 AN: 67892

Other (OTH) AF: 0.239 AC: 503 AN: 2102

Alfa AF: 0.145 Hom.: 576

Bravo AF: 0.240

Asia WGS AF: 0.205 AC: 715 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	0.27
DANN	Benign	0.36
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2097677; hg19: chr7-22732839;