11-2287532-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 0.825 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.826 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

Gnomad4 AFR AF: 0.713

Gnomad4 AMR AF: 0.723

Gnomad4 ASJ AF: 0.941

Gnomad4 EAS AF: 0.529

Gnomad4 SAS AF: 0.869

Gnomad4 FIN AF: 0.844

Gnomad4 NFE AF: 0.924

Gnomad4 OTH AF: 0.841

Alfa AF: 0.906 Hom.: 120905

Bravo AF: 0.812

Asia WGS AF: 0.707 AC: 2461 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	3.6
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2521263; hg19: chr11-2308762;