rs6766709

Positions:

• chr3-137051421-A-T

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.137051421A>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;