rs9666583

Variant names:

• chr11-55341535-T-A
• rs9666583

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 0.367 in 151,978 control chromosomes in the GnomAD database, including 10,717 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 0.37 (10717 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.33
• Publications: 0 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 = 0.462 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: 0.367 AC: 55685 AN: 151862 Hom.: 10702 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.370

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.359

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

GnomAD4 genome AF: 0.367 AC: 55733 AN: 151978 Hom.: 10717 Cov.: 32 AF XY: 0.364 AC XY: 27022 AN XY: 74256

African (AFR) AF: 0.468 AC: 19393 AN: 41444

American (AMR) AF: 0.265 AC: 4045 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.308 AC: 1069 AN: 3470

East Asian (EAS) AF: 0.234 AC: 1203 AN: 5152

South Asian (SAS) AF: 0.225 AC: 1089 AN: 4830

European-Finnish (FIN) AF: 0.368 AC: 3890 AN: 10562

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.351 AC: 23854 AN: 67938

Other (OTH) AF: 0.353 AC: 747 AN: 2114

Alfa AF: 0.371 Hom.: 1380

Bravo AF: 0.365

Asia WGS AF: 0.236 AC: 819 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.43
DANN	Benign	0.39
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs9666583; hg19: chr11-55109011;