11-68659776-A-G

Variant names:

• chr11-68659776-A-G
• rs2156464

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 0.865 in 152,196 control chromosomes in the GnomAD database, including 57,129 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 (57129 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.929 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: 0.865 AC: 131538 AN: 152078 Hom.: 57069 Cov.: 31

Gnomad AFR AF: 0.937

Gnomad AMI AF: 0.697

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.854

Gnomad SAS AF: 0.868

Gnomad FIN AF: 0.901

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.825

Gnomad OTH AF: 0.851

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

GnomAD4 genome AF: 0.865 AC: 131656 AN: 152196 Hom.: 57129 Cov.: 31 AF XY: 0.869 AC XY: 64630 AN XY: 74404

African (AFR) AF: 0.937 AC: 38929 AN: 41542

American (AMR) AF: 0.827 AC: 12653 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3123 AN: 3472

East Asian (EAS) AF: 0.854 AC: 4392 AN: 5144

South Asian (SAS) AF: 0.868 AC: 4185 AN: 4822

European-Finnish (FIN) AF: 0.901 AC: 9557 AN: 10604

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.825 AC: 56120 AN: 68002

Other (OTH) AF: 0.853 AC: 1799 AN: 2108

Alfa AF: 0.840 Hom.: 28137

Bravo AF: 0.858

Asia WGS AF: 0.899 AC: 3124 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.20
DANN	Benign	0.37
PhyloP100		0.089

Splicing

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

Other links and lift over

dbSNP: rs2156464; hg19: chr11-68427244;