rs9666583

chr11-55341535-T-A

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 0.367 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

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 = 0.462 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: 0.367 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

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.265

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.368

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.353

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.43
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9666583; hg19: chr11-55109011;