11-116799960-A-C

Variant names:

• chr11-116799960-A-C
• rs6589567

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 0.87 in 150,824 control chromosomes in the GnomAD database, including 57,569 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 0.87 (57569 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.457
• Publications: 36 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 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: 0.870 AC: 131174 AN: 150708 Hom.: 57525 Cov.: 31

Gnomad AFR AF: 0.913

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.824

Gnomad ASJ AF: 0.858

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.758

Gnomad FIN AF: 0.824

Gnomad MID AF: 0.841

Gnomad NFE AF: 0.882

Gnomad OTH AF: 0.866

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

GnomAD4 genome AF: 0.870 AC: 131270 AN: 150824 Hom.: 57569 Cov.: 31 AF XY: 0.864 AC XY: 63691 AN XY: 73724

African (AFR) AF: 0.914 AC: 36735 AN: 40206

American (AMR) AF: 0.823 AC: 12551 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.858 AC: 2980 AN: 3472

East Asian (EAS) AF: 0.718 AC: 3712 AN: 5168

South Asian (SAS) AF: 0.757 AC: 3648 AN: 4818

European-Finnish (FIN) AF: 0.824 AC: 8737 AN: 10602

Middle Eastern (MID) AF: 0.839 AC: 245 AN: 292

European-Non Finnish (NFE) AF: 0.883 AC: 60016 AN: 68006

Other (OTH) AF: 0.861 AC: 1811 AN: 2104

Alfa AF: 0.871 Hom.: 56009

Bravo AF: 0.876

Asia WGS AF: 0.732 AC: 2546 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs6589567; hg19: chr11-116670676;