rs9552790

Variant names:

• chr13-22992008-G-A
• rs9552790

Variant summary

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

The variant allele was found at a frequency of 0.0842 in 151,918 control chromosomes in the GnomAD database, including 795 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 0.084 (795 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 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

Frequencies

GnomAD3 genomes AF: 0.0842 AC: 12785 AN: 151800 Hom.: 797 Cov.: 30

Gnomad AFR AF: 0.0735

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0640

Gnomad ASJ AF: 0.0577

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0598

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0730

Gnomad OTH AF: 0.0829

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

GnomAD4 genome AF: 0.0842 AC: 12794 AN: 151918 Hom.: 795 Cov.: 30 AF XY: 0.0860 AC XY: 6387 AN XY: 74244

African (AFR) AF: 0.0736 AC: 3050 AN: 41442

American (AMR) AF: 0.0639 AC: 975 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0577 AC: 200 AN: 3466

East Asian (EAS) AF: 0.372 AC: 1907 AN: 5128

South Asian (SAS) AF: 0.154 AC: 743 AN: 4810

European-Finnish (FIN) AF: 0.0598 AC: 630 AN: 10528

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0730 AC: 4964 AN: 67974

Other (OTH) AF: 0.0844 AC: 178 AN: 2108

Alfa AF: 0.0713 Hom.: 123

Bravo AF: 0.0824

Asia WGS AF: 0.230 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.3
DANN	Benign	0.88
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9552790; hg19: chr13-23566147;