rs2798062

Variant names:

• chr9-90270325-G-A
• rs2798062

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 0.225 in 152,108 control chromosomes in the GnomAD database, including 4,267 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 0.22 (4267 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.265 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: 0.225 AC: 34190 AN: 151990 Hom.: 4266 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.167

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.268

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.225 AC: 34192 AN: 152108 Hom.: 4267 Cov.: 32 AF XY: 0.227 AC XY: 16893 AN XY: 74350

African (AFR) AF: 0.134 AC: 5579 AN: 41494

American (AMR) AF: 0.200 AC: 3058 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.224 AC: 776 AN: 3472

East Asian (EAS) AF: 0.217 AC: 1121 AN: 5170

South Asian (SAS) AF: 0.165 AC: 794 AN: 4822

European-Finnish (FIN) AF: 0.362 AC: 3826 AN: 10560

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.268 AC: 18239 AN: 67988

Other (OTH) AF: 0.226 AC: 478 AN: 2112

Alfa AF: 0.249 Hom.: 3163

Bravo AF: 0.210

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.1
DANN	Benign	0.26
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs2798062; hg19: chr9-93032607;