9-102679835-A-G

Variant names:

• chr9-102679835-A-G
• rs2210533

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 0.802 in 152,126 control chromosomes in the GnomAD database, including 49,108 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 0.80 (49108 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.801 AC: 121820 AN: 152010 Hom.: 49049 Cov.: 31

Gnomad AFR AF: 0.828

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.843

Gnomad ASJ AF: 0.773

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.914

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.759

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.802 AC: 121939 AN: 152126 Hom.: 49108 Cov.: 31 AF XY: 0.808 AC XY: 60074 AN XY: 74370

African (AFR) AF: 0.828 AC: 34367 AN: 41512

American (AMR) AF: 0.844 AC: 12882 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.773 AC: 2685 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5144 AN: 5156

South Asian (SAS) AF: 0.914 AC: 4412 AN: 4828

European-Finnish (FIN) AF: 0.776 AC: 8209 AN: 10584

Middle Eastern (MID) AF: 0.699 AC: 204 AN: 292

European-Non Finnish (NFE) AF: 0.759 AC: 51602 AN: 67996

Other (OTH) AF: 0.809 AC: 1703 AN: 2106

Alfa AF: 0.780 Hom.: 74499

Bravo AF: 0.808

Asia WGS AF: 0.947 AC: 3289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.56
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs2210533; hg19: chr9-105442117;