rs3129766

Variant names:

• chr6-32626664-A-G
• rs3129766

Your query was ambiguous. Multiple possible variants found:

• chr6-32626664-A-G
• chr6-32626664-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 0.442 in 98,724 control chromosomes in the GnomAD database, including 9,873 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 0.44 (9873 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.112
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.501 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: 0.442 AC: 43603 AN: 98634 Hom.: 9866 Cov.: 23

Gnomad AFR AF: 0.326

Gnomad AMI AF: 0.571

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.571

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.543

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.442 AC: 43635 AN: 98724 Hom.: 9873 Cov.: 23 AF XY: 0.435 AC XY: 21023 AN XY: 48368

African (AFR) AF: 0.326 AC: 8866 AN: 27196

American (AMR) AF: 0.513 AC: 5041 AN: 9834

Ashkenazi Jewish (ASJ) AF: 0.571 AC: 1225 AN: 2144

East Asian (EAS) AF: 0.502 AC: 2015 AN: 4012

South Asian (SAS) AF: 0.407 AC: 1249 AN: 3066

European-Finnish (FIN) AF: 0.392 AC: 2588 AN: 6610

Middle Eastern (MID) AF: 0.533 AC: 80 AN: 150

European-Non Finnish (NFE) AF: 0.494 AC: 21617 AN: 43802

Other (OTH) AF: 0.463 AC: 584 AN: 1262

Alfa AF: 0.300 Hom.: 862

Bravo AF: 0.302

Asia WGS AF: 0.313 AC: 1091 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.7
DANN	Benign	0.48
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs3129766; hg19: chr6-32594441;