chr11-133697090-C-T

Variant names:

• chr11-133697090-C-T
• rs4397868

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;