11-126186413-C-T

Variant names:

• chr11-126186413-C-T
• rs12419184

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.18
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0678 AC: 2808 AN: 41424

American (AMR) AF: 0.180 AC: 2749 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3466

East Asian (EAS) AF: 0.0483 AC: 247 AN: 5118

South Asian (SAS) AF: 0.151 AC: 727 AN: 4800

European-Finnish (FIN) AF: 0.100 AC: 1057 AN: 10560

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 292

European-Non Finnish (NFE) AF: 0.0832 AC: 5651 AN: 67936

Other (OTH) AF: 0.113 AC: 237 AN: 2104

Alfa AF: 0.0433 Hom.: 34

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
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs12419184; hg19: chr11-126056308;