11-126186413-C-T

Position:

• chr11-126186413-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 0.0932 in 151,888 control chromosomes in the GnomAD database, including 851 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 0.093 (851 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.126186413C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0932 AC: 14138 AN: 151768 Hom.: 852 Cov.: 33

Gnomad AFR AF: 0.0677

Gnomad AMI AF: 0.0659

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0482

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.100

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.0832

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.0932 AC: 14150 AN: 151888 Hom.: 851 Cov.: 33 AF XY: 0.0958 AC XY: 7113 AN XY: 74240

Gnomad4 AFR AF: 0.0678

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.166

Gnomad4 EAS AF: 0.0483

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.100

Gnomad4 NFE AF: 0.0832

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0421 Hom.: 32

Bravo AF: 0.101

Asia WGS AF: 0.128 AC: 447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12419184; hg19: chr11-126056308;