11-116829268-A-C

Variant names:

• chr11-116829268-A-C
• rs2542052

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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 0.66 (21236 hom., cov: 19)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 38 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.697 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: 0.657 AC: 77042 AN: 117188 Hom.: 21243 Cov.: 19

Gnomad AFR AF: 0.534

Gnomad AMI AF: 0.739

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.661

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.607

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.656

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

GnomAD4 genome AF: 0.657 AC: 77063 AN: 117254 Hom.: 21236 Cov.: 19 AF XY: 0.652 AC XY: 37081 AN XY: 56912

African (AFR) AF: 0.534 AC: 12972 AN: 24292

American (AMR) AF: 0.674 AC: 8314 AN: 12334

Ashkenazi Jewish (ASJ) AF: 0.661 AC: 1928 AN: 2918

East Asian (EAS) AF: 0.651 AC: 2666 AN: 4094

South Asian (SAS) AF: 0.606 AC: 2202 AN: 3632

European-Finnish (FIN) AF: 0.688 AC: 5782 AN: 8402

Middle Eastern (MID) AF: 0.664 AC: 154 AN: 232

European-Non Finnish (NFE) AF: 0.702 AC: 41357 AN: 58874

Other (OTH) AF: 0.654 AC: 1091 AN: 1668

Alfa AF: 0.587 Hom.: 72079

Bravo AF: 0.520

Asia WGS AF: 0.490 AC: 1698 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.35
PhyloP100		0.036
PromoterAI		0.0038	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2542052; hg19: chr11-116699984;