chr11-92993313-G-A

Variant names:

• chr11-92993313-G-A
• rs9666752

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 0.54 in 152,024 control chromosomes in the GnomAD database, including 22,510 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 0.54 (22510 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.682 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: 0.540 AC: 81975 AN: 151906 Hom.: 22479 Cov.: 33

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.438

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.540 AC: 82067 AN: 152024 Hom.: 22510 Cov.: 33 AF XY: 0.549 AC XY: 40764 AN XY: 74292

African (AFR) AF: 0.525 AC: 21786 AN: 41468

American (AMR) AF: 0.642 AC: 9807 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.438 AC: 1519 AN: 3470

East Asian (EAS) AF: 0.701 AC: 3626 AN: 5172

South Asian (SAS) AF: 0.664 AC: 3191 AN: 4806

European-Finnish (FIN) AF: 0.564 AC: 5958 AN: 10560

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34278 AN: 67964

Other (OTH) AF: 0.529 AC: 1118 AN: 2114

Alfa AF: 0.487 Hom.: 5516

Bravo AF: 0.546

Asia WGS AF: 0.637 AC: 2215 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	0.14
DANN	Benign	0.27
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs9666752; hg19: chr11-92726479;