6-43759219-T-C

Variant names:

• chr6-43759219-T-C
• rs866236

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 0.654 in 152,012 control chromosomes in the GnomAD database, including 33,918 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 0.65 (33918 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.37
• Publications: 14 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 (NFE) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.654 AC: 99373 AN: 151894 Hom.: 33904 Cov.: 32

Gnomad AFR AF: 0.467

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.810

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.771

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.763

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.654 AC: 99405 AN: 152012 Hom.: 33918 Cov.: 32 AF XY: 0.649 AC XY: 48247 AN XY: 74298

African (AFR) AF: 0.466 AC: 19320 AN: 41420

American (AMR) AF: 0.633 AC: 9668 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.810 AC: 2806 AN: 3466

East Asian (EAS) AF: 0.493 AC: 2542 AN: 5160

South Asian (SAS) AF: 0.582 AC: 2800 AN: 4810

European-Finnish (FIN) AF: 0.771 AC: 8166 AN: 10598

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.763 AC: 51860 AN: 67970

Other (OTH) AF: 0.665 AC: 1404 AN: 2110

Alfa AF: 0.733 Hom.: 92846

Bravo AF: 0.640

Asia WGS AF: 0.478 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.014
DANN	Benign	0.65
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs866236; hg19: chr6-43726956;