11-20334898-G-A

Variant names:

• chr11-20334898-G-A
• rs7128099

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 0.712 in 151,900 control chromosomes in the GnomAD database, including 40,524 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 0.71 (40524 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108141 AN: 151790 Hom.: 40515 Cov.: 30

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.850

Gnomad EAS AF: 0.277

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.816

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.712 AC: 108175 AN: 151900 Hom.: 40524 Cov.: 30 AF XY: 0.710 AC XY: 52693 AN XY: 74242

African (AFR) AF: 0.520 AC: 21495 AN: 41342

American (AMR) AF: 0.692 AC: 10564 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.850 AC: 2949 AN: 3470

East Asian (EAS) AF: 0.277 AC: 1428 AN: 5156

South Asian (SAS) AF: 0.742 AC: 3573 AN: 4814

European-Finnish (FIN) AF: 0.816 AC: 8620 AN: 10568

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56950 AN: 67964

Other (OTH) AF: 0.751 AC: 1587 AN: 2114

Alfa AF: 0.784 Hom.: 108437

Bravo AF: 0.695

Asia WGS AF: 0.577 AC: 2010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.49
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs7128099; hg19: chr11-20356444;