rs9552790

chr13-22992008-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 0.0842 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0736

Gnomad4 AMR AF: 0.0639

Gnomad4 ASJ AF: 0.0577

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.0598

Gnomad4 NFE AF: 0.0730

Gnomad4 OTH AF: 0.0844

Alfa AF: 0.0713 Hom.: 73

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9552790; hg19: chr13-23566147;