rs6766709

Variant names:

• chr3-137051421-A-T
• rs6766709

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 0.797 in 152,178 control chromosomes in the GnomAD database, including 49,086 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 (49086 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

ACMG classification

Verdict is Benign. Variant got -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 = 0.92 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: 0.797 AC: 121230 AN: 152060 Hom.: 49043 Cov.: 33

Gnomad AFR AF: 0.927

Gnomad AMI AF: 0.645

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.792

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.760

Gnomad MID AF: 0.839

Gnomad NFE AF: 0.761

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.797 AC: 121321 AN: 152178 Hom.: 49086 Cov.: 33 AF XY: 0.795 AC XY: 59117 AN XY: 74376

Gnomad4 AFR AF: 0.928

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.792

Gnomad4 EAS AF: 0.518

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.760

Gnomad4 NFE AF: 0.761

Gnomad4 OTH AF: 0.777

Alfa AF: 0.789 Hom.: 5916

Bravo AF: 0.798

Asia WGS AF: 0.657 AC: 2289 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.2
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6766709; hg19: chr3-136770263;