11-118685689-G-A

Variant names:

• chr11-118685689-G-A
• rs11216943

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 0.204 in 151,996 control chromosomes in the GnomAD database, including 3,355 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 0.20 (3355 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 16 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 (SAS) allele frequency at 95% confidence interval = 0.339 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: 0.204 AC: 30926 AN: 151878 Hom.: 3352 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.176

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.199

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

GnomAD4 genome AF: 0.204 AC: 30934 AN: 151996 Hom.: 3355 Cov.: 31 AF XY: 0.206 AC XY: 15313 AN XY: 74286

African (AFR) AF: 0.123 AC: 5102 AN: 41460

American (AMR) AF: 0.209 AC: 3183 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.214 AC: 743 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1167 AN: 5150

South Asian (SAS) AF: 0.353 AC: 1700 AN: 4820

European-Finnish (FIN) AF: 0.235 AC: 2485 AN: 10572

Middle Eastern (MID) AF: 0.221 AC: 65 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15905 AN: 67944

Other (OTH) AF: 0.201 AC: 424 AN: 2110

Alfa AF: 0.224 Hom.: 5821

Bravo AF: 0.191

Asia WGS AF: 0.262 AC: 910 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	2.7
DANN	Benign	0.47
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs11216943; hg19: chr11-118556398;