11-132411757-C-T

Variant names:

• chr11-132411757-C-T
• rs1940013

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 0.289 in 152,058 control chromosomes in the GnomAD database, including 6,480 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 0.29 (6480 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.306 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: 0.289 AC: 43947 AN: 151940 Hom.: 6474 Cov.: 33

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.310

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.289 AC: 43977 AN: 152058 Hom.: 6480 Cov.: 33 AF XY: 0.291 AC XY: 21658 AN XY: 74344

African (AFR) AF: 0.252 AC: 10454 AN: 41466

American (AMR) AF: 0.311 AC: 4747 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.192 AC: 667 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1094 AN: 5162

South Asian (SAS) AF: 0.219 AC: 1053 AN: 4810

European-Finnish (FIN) AF: 0.397 AC: 4193 AN: 10566

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.310 AC: 21066 AN: 67984

Other (OTH) AF: 0.252 AC: 533 AN: 2114

Alfa AF: 0.279 Hom.: 3174

Bravo AF: 0.276

Asia WGS AF: 0.225 AC: 781 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.17
DANN	Benign	0.50
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs1940013; hg19: chr11-132281651;