rs2797634

Variant names:

• chr9-102878369-G-A
• rs2797634

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 0.639 in 151,788 control chromosomes in the GnomAD database, including 31,598 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 0.64 (31598 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 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: 0.638 AC: 96828 AN: 151670 Hom.: 31554 Cov.: 31

Gnomad AFR AF: 0.730

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.627

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.674

Gnomad NFE AF: 0.563

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.639 AC: 96932 AN: 151788 Hom.: 31598 Cov.: 31 AF XY: 0.643 AC XY: 47639 AN XY: 74138

Gnomad4 AFR AF: 0.730

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.627

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.757

Gnomad4 FIN AF: 0.521

Gnomad4 NFE AF: 0.563

Gnomad4 OTH AF: 0.663

Alfa AF: 0.590 Hom.: 14287

Bravo AF: 0.657

Asia WGS AF: 0.824 AC: 2861 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2797634; hg19: chr9-105640651;