rs9666789

chr11-92898924-G-Achr11-92898924-G-T

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 0.446 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.446 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

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.395

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.480

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.364

Gnomad4 OTH AF: 0.442

Alfa AF: 0.391 Hom.: 6842

Bravo AF: 0.464

Asia WGS AF: 0.548 AC: 1903 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	5.8
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9666789; hg19: chr11-92632090;