chr9-102878369-G-A

Variant names:

• chr9-102878369-G-A
• rs2797634

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 0.639 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.730 AC: 30225 AN: 41418

American (AMR) AF: 0.714 AC: 10859 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.627 AC: 2176 AN: 3472

East Asian (EAS) AF: 0.827 AC: 4247 AN: 5136

South Asian (SAS) AF: 0.757 AC: 3646 AN: 4818

European-Finnish (FIN) AF: 0.521 AC: 5484 AN: 10528

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.563 AC: 38207 AN: 67890

Other (OTH) AF: 0.663 AC: 1398 AN: 2108

Alfa AF: 0.592 Hom.: 15902

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs2797634; hg19: chr9-105640651;