11-69185586-G-A

Variant names:

• chr11-69185586-G-A
• rs7128814

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 0.662 in 151,638 control chromosomes in the GnomAD database, including 34,477 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 0.66 (34477 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.308
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 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: 0.662 AC: 100253 AN: 151524 Hom.: 34420 Cov.: 30

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.631

Gnomad SAS AF: 0.480

Gnomad FIN AF: 0.561

Gnomad MID AF: 0.668

Gnomad NFE AF: 0.589

Gnomad OTH AF: 0.665

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

GnomAD4 genome AF: 0.662 AC: 100371 AN: 151638 Hom.: 34477 Cov.: 30 AF XY: 0.657 AC XY: 48589 AN XY: 74008

African (AFR) AF: 0.869 AC: 35975 AN: 41414

American (AMR) AF: 0.566 AC: 8626 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.633 AC: 2196 AN: 3470

East Asian (EAS) AF: 0.631 AC: 3254 AN: 5160

South Asian (SAS) AF: 0.481 AC: 2310 AN: 4804

European-Finnish (FIN) AF: 0.561 AC: 5788 AN: 10326

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.589 AC: 39973 AN: 67908

Other (OTH) AF: 0.668 AC: 1403 AN: 2100

Alfa AF: 0.612 Hom.: 28221

Bravo AF: 0.678

Asia WGS AF: 0.618 AC: 2144 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.68
DANN	Benign	0.47
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs7128814; hg19: chr11-68953054;