rs6786129

Positions:

• chr3-143194855-A-G
• chr3-143194855-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 0.778 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.755

Alfa AF: 0.760 Hom.: 7173

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6786129; hg19: chr3-142913697;