7-22691090-G-A

Position:

• chr7-22691090-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.803 in 152,128 control chromosomes in the GnomAD database, including 51,551 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 0.80 (51551 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.22691090G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000650428.1	n.46+36478C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.804 AC: 122179 AN: 152010 Hom.: 51549 Cov.: 31

Gnomad AFR AF: 0.604

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.780

Gnomad ASJ AF: 0.915

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.939

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.803 AC: 122203 AN: 152128 Hom.: 51551 Cov.: 31 AF XY: 0.799 AC XY: 59411 AN XY: 74376

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.780

Gnomad4 ASJ AF: 0.915

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.678

Gnomad4 FIN AF: 0.939

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.819

Alfa AF: 0.911 Hom.: 125400

Bravo AF: 0.783

Asia WGS AF: 0.517 AC: 1803 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	3.2
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1476482; hg19: chr7-22730709;