rs9682099

Variant names:

• chr3-147777772-G-A
• rs9682099

Your query was ambiguous. Multiple possible variants found:

• chr3-147777772-G-A
• chr3-147777772-G-T

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 0.262 in 151,910 control chromosomes in the GnomAD database, including 6,865 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 0.26 (6865 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.985
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.487 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: 0.262 AC: 39801 AN: 151792 Hom.: 6840 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.262 AC: 39869 AN: 151910 Hom.: 6865 Cov.: 32 AF XY: 0.258 AC XY: 19149 AN XY: 74222

African (AFR) AF: 0.493 AC: 20408 AN: 41390

American (AMR) AF: 0.222 AC: 3379 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 566 AN: 3468

East Asian (EAS) AF: 0.213 AC: 1098 AN: 5156

South Asian (SAS) AF: 0.155 AC: 746 AN: 4810

European-Finnish (FIN) AF: 0.140 AC: 1476 AN: 10560

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11482 AN: 67964

Other (OTH) AF: 0.237 AC: 500 AN: 2110

Alfa AF: 0.194 Hom.: 5771

Bravo AF: 0.276

Asia WGS AF: 0.221 AC: 769 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.46
DANN	Benign	0.22
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs9682099; hg19: chr3-147495559;