11-118687746-A-G

Position:

• chr11-118687746-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.361

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.187

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.333

Alfa AF: 0.327 Hom.: 1033

Bravo AF: 0.333

Asia WGS AF: 0.270 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs558907; hg19: chr11-118558455;