chr11-118687746-A-G

Variant names:

• chr11-118687746-A-G
• rs558907

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 0.317 in 151,550 control chromosomes in the GnomAD database, including 7,989 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 0.32 (7989 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.69
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48073 AN: 151432 Hom.: 7975 Cov.: 31

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.482

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.361

Gnomad EAS AF: 0.403

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.317 AC: 48105 AN: 151550 Hom.: 7989 Cov.: 31 AF XY: 0.317 AC XY: 23504 AN XY: 74038

African (AFR) AF: 0.248 AC: 10276 AN: 41370

American (AMR) AF: 0.459 AC: 6979 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.361 AC: 1250 AN: 3460

East Asian (EAS) AF: 0.404 AC: 2076 AN: 5142

South Asian (SAS) AF: 0.187 AC: 901 AN: 4808

European-Finnish (FIN) AF: 0.311 AC: 3258 AN: 10474

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22121 AN: 67782

Other (OTH) AF: 0.333 AC: 701 AN: 2106

Alfa AF: 0.325 Hom.: 1061

Bravo AF: 0.333

Asia WGS AF: 0.270 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.1
DANN	Benign	0.64
PhyloP100		-2.7

Splicing

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

Other links and lift over

dbSNP: rs558907; hg19: chr11-118558455;