11-116801515-A-G

Variant names:

• chr11-116801515-A-G
• rs2542061

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 0.393 in 150,918 control chromosomes in the GnomAD database, including 13,795 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 0.39 (13795 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.516 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: 0.394 AC: 59351 AN: 150800 Hom.: 13800 Cov.: 31

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.573

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.363

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.393 AC: 59349 AN: 150918 Hom.: 13795 Cov.: 31 AF XY: 0.386 AC XY: 28503 AN XY: 73778

African (AFR) AF: 0.163 AC: 6602 AN: 40400

American (AMR) AF: 0.387 AC: 5892 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1660 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1943 AN: 5176

South Asian (SAS) AF: 0.363 AC: 1751 AN: 4830

European-Finnish (FIN) AF: 0.439 AC: 4629 AN: 10542

Middle Eastern (MID) AF: 0.373 AC: 109 AN: 292

European-Non Finnish (NFE) AF: 0.520 AC: 35364 AN: 67966

Other (OTH) AF: 0.419 AC: 879 AN: 2096

Alfa AF: 0.346 Hom.: 4566

Bravo AF: 0.384

Asia WGS AF: 0.347 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.4
DANN	Benign	0.66
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs2542061; hg19: chr11-116672231;