chr11-116792991-G-A

Variant names:

• chr11-116792991-G-A
• rs662799

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 0.899 in 152,224 control chromosomes in the GnomAD database, including 61,676 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 0.90 (61676 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 571 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.929 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.899 AC: 136711 AN: 152106 Hom.: 61657 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.935

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.912

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.935

Gnomad OTH AF: 0.890

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

GnomAD4 genome AF: 0.899 AC: 136785 AN: 152224 Hom.: 61676 Cov.: 32 AF XY: 0.895 AC XY: 66601 AN XY: 74420

African (AFR) AF: 0.880 AC: 36529 AN: 41522

American (AMR) AF: 0.867 AC: 13255 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.912 AC: 3165 AN: 3472

East Asian (EAS) AF: 0.698 AC: 3616 AN: 5178

South Asian (SAS) AF: 0.811 AC: 3913 AN: 4826

European-Finnish (FIN) AF: 0.921 AC: 9762 AN: 10604

Middle Eastern (MID) AF: 0.881 AC: 259 AN: 294

European-Non Finnish (NFE) AF: 0.935 AC: 63564 AN: 68012

Other (OTH) AF: 0.885 AC: 1871 AN: 2114

Alfa AF: 0.914 Hom.: 130385

Bravo AF: 0.894

Asia WGS AF: 0.767 AC: 2668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.49
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs662799; hg19: chr11-116663707;