rs6786129

Variant names:

• chr3-143194855-A-G
• rs6786129

Your query was ambiguous. Multiple possible variants found:

• chr3-143194855-A-G
• chr3-143194855-A-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 0.778 in 151,930 control chromosomes in the GnomAD database, including 46,835 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 0.78 (46835 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 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: 0.778 AC: 118041 AN: 151812 Hom.: 46771 Cov.: 29

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.710

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.570

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.754

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

GnomAD4 genome AF: 0.778 AC: 118161 AN: 151930 Hom.: 46835 Cov.: 29 AF XY: 0.774 AC XY: 57515 AN XY: 74274

African (AFR) AF: 0.932 AC: 38603 AN: 41436

American (AMR) AF: 0.763 AC: 11653 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2198 AN: 3472

East Asian (EAS) AF: 0.786 AC: 4069 AN: 5180

South Asian (SAS) AF: 0.569 AC: 2732 AN: 4802

European-Finnish (FIN) AF: 0.738 AC: 7754 AN: 10510

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48718 AN: 67948

Other (OTH) AF: 0.755 AC: 1595 AN: 2112

Alfa AF: 0.764 Hom.: 7506

Bravo AF: 0.794

Asia WGS AF: 0.695 AC: 2417 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		-0.050

Splicing

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

Other links and lift over

dbSNP: rs6786129; hg19: chr3-142913697;