6-32839676-A-G

Variant names:

• chr6-32839676-A-G
• rs3763365

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 0.474 in 151,772 control chromosomes in the GnomAD database, including 17,296 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 0.47 (17296 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0810
• Publications: 20 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.475 AC: 71965 AN: 151654 Hom.: 17292 Cov.: 32

Gnomad AFR AF: 0.433

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.479

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.473

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

GnomAD4 genome AF: 0.474 AC: 71992 AN: 151772 Hom.: 17296 Cov.: 32 AF XY: 0.474 AC XY: 35115 AN XY: 74150

African (AFR) AF: 0.433 AC: 17914 AN: 41356

American (AMR) AF: 0.479 AC: 7325 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 1394 AN: 3468

East Asian (EAS) AF: 0.582 AC: 3006 AN: 5168

South Asian (SAS) AF: 0.526 AC: 2526 AN: 4806

European-Finnish (FIN) AF: 0.454 AC: 4771 AN: 10510

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.492 AC: 33393 AN: 67878

Other (OTH) AF: 0.469 AC: 990 AN: 2110

Alfa AF: 0.484 Hom.: 14535

Bravo AF: 0.474

Asia WGS AF: 0.511 AC: 1777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.2
DANN	Benign	0.45
PhyloP100		-0.081

Splicing

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

Other links and lift over

dbSNP: rs3763365; hg19: chr6-32807453;