rs709159

chr3-12439704-C-Achr3-12439704-C-G

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 0.785 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.902

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.735

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.801

Gnomad4 NFE AF: 0.758

Gnomad4 OTH AF: 0.769

Alfa AF: 0.770 Hom.: 28464

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs709159; hg19: chr3-12481203;