11-2287532-A-G

Variant names:

• chr11-2287532-A-G
• rs2521263

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 0.825 in 150,342 control chromosomes in the GnomAD database, including 52,194 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 0.83 (52194 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.918 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: 0.826 AC: 124059 AN: 150224 Hom.: 52186 Cov.: 26

Gnomad AFR AF: 0.713

Gnomad AMI AF: 0.948

Gnomad AMR AF: 0.724

Gnomad ASJ AF: 0.941

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.870

Gnomad FIN AF: 0.844

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.924

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.825 AC: 124107 AN: 150342 Hom.: 52194 Cov.: 26 AF XY: 0.820 AC XY: 60097 AN XY: 73312

African (AFR) AF: 0.713 AC: 28965 AN: 40640

American (AMR) AF: 0.723 AC: 10943 AN: 15130

Ashkenazi Jewish (ASJ) AF: 0.941 AC: 3248 AN: 3452

East Asian (EAS) AF: 0.529 AC: 2676 AN: 5054

South Asian (SAS) AF: 0.869 AC: 4136 AN: 4758

European-Finnish (FIN) AF: 0.844 AC: 8666 AN: 10272

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.924 AC: 62608 AN: 67756

Other (OTH) AF: 0.841 AC: 1749 AN: 2080

Alfa AF: 0.892 Hom.: 265401

Bravo AF: 0.812

Asia WGS AF: 0.707 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.6
DANN	Benign	0.29
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs2521263; hg19: chr11-2308762;