11-113385608-C-T

Variant names:

• chr11-113385608-C-T
• rs877137

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 0.373 in 152,084 control chromosomes in the GnomAD database, including 12,811 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 (12811 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 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: 0.373 AC: 56720 AN: 151966 Hom.: 12824 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.542

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.521

Gnomad EAS AF: 0.0562

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.439

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.430

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

GnomAD4 genome AF: 0.373 AC: 56713 AN: 152084 Hom.: 12811 Cov.: 32 AF XY: 0.366 AC XY: 27185 AN XY: 74362

Gnomad4 AFR AF: 0.155

Gnomad4 AMR AF: 0.323

Gnomad4 ASJ AF: 0.521

Gnomad4 EAS AF: 0.0557

Gnomad4 SAS AF: 0.372

Gnomad4 FIN AF: 0.439

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.427

Alfa AF: 0.323 Hom.: 1181

Bravo AF: 0.354

Asia WGS AF: 0.201 AC: 700 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs877137; hg19: chr11-113256330;