rs9666789

Variant names:

• chr11-92898924-G-A
• rs9666789

Your query was ambiguous. Multiple possible variants found:

• chr11-92898924-G-A
• chr11-92898924-G-T

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 0.446 in 151,810 control chromosomes in the GnomAD database, including 15,806 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 0.45 (15806 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.477
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.547 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: 0.446 AC: 67603 AN: 151692 Hom.: 15757 Cov.: 31

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.479

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.446 AC: 67719 AN: 151810 Hom.: 15806 Cov.: 31 AF XY: 0.449 AC XY: 33267 AN XY: 74160

African (AFR) AF: 0.553 AC: 22895 AN: 41386

American (AMR) AF: 0.530 AC: 8095 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1372 AN: 3470

East Asian (EAS) AF: 0.538 AC: 2759 AN: 5128

South Asian (SAS) AF: 0.480 AC: 2309 AN: 4814

European-Finnish (FIN) AF: 0.386 AC: 4045 AN: 10492

Middle Eastern (MID) AF: 0.421 AC: 122 AN: 290

European-Non Finnish (NFE) AF: 0.364 AC: 24710 AN: 67936

Other (OTH) AF: 0.442 AC: 930 AN: 2104

Alfa AF: 0.400 Hom.: 11085

Bravo AF: 0.464

Asia WGS AF: 0.548 AC: 1903 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	5.8
DANN	Benign	0.50
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs9666789; hg19: chr11-92632090;