rs709159

Variant names:

• chr3-12439704-C-A
• rs709159

Your query was ambiguous. Multiple possible variants found:

• chr3-12439704-C-A
• chr3-12439704-C-G

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 0.785 in 152,134 control chromosomes in the GnomAD database, including 47,707 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 0.79 (47707 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.53).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.894 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: 0.785 AC: 119398 AN: 152016 Hom.: 47660 Cov.: 32

Gnomad AFR AF: 0.901

Gnomad AMI AF: 0.873

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.735

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.801

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.758

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.785 AC: 119498 AN: 152134 Hom.: 47707 Cov.: 32 AF XY: 0.780 AC XY: 57985 AN XY: 74340

African (AFR) AF: 0.902 AC: 37446 AN: 41528

American (AMR) AF: 0.762 AC: 11652 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.735 AC: 2552 AN: 3470

East Asian (EAS) AF: 0.525 AC: 2717 AN: 5174

South Asian (SAS) AF: 0.527 AC: 2532 AN: 4804

European-Finnish (FIN) AF: 0.801 AC: 8449 AN: 10554

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.758 AC: 51514 AN: 67996

Other (OTH) AF: 0.769 AC: 1626 AN: 2114

Alfa AF: 0.779 Hom.: 48035

Bravo AF: 0.792

Asia WGS AF: 0.600 AC: 2089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	12
DANN	Benign	0.68
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs709159; hg19: chr3-12481203;