rs2797634

Positions:

• chr9-102878369-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 0.639 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;