11-133697090-C-T

Position:

• chr11-133697090-C-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 0.871 in 152,244 control chromosomes in the GnomAD database, including 58,176 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 0.87 (58176 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.133697090C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132526 AN: 152126 Hom.: 58115 Cov.: 32

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.871 AC: 132647 AN: 152244 Hom.: 58176 Cov.: 32 AF XY: 0.872 AC XY: 64932 AN XY: 74426

Gnomad4 AFR AF: 0.963

Gnomad4 AMR AF: 0.904

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.922

Gnomad4 FIN AF: 0.815

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.886

Alfa AF: 0.829 Hom.: 115043

Bravo AF: 0.881

Asia WGS AF: 0.942 AC: 3276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.078
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4397868; hg19: chr11-133566985;