chr11-113882290-C-T

Variant names:

• chr11-113882290-C-T
• rs869451

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 0.504 in 152,112 control chromosomes in the GnomAD database, including 19,883 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 0.50 (19883 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.266
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.607 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: 0.504 AC: 76551 AN: 151994 Hom.: 19847 Cov.: 33

Gnomad AFR AF: 0.613

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.531

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.421

Gnomad OTH AF: 0.501

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

GnomAD4 genome AF: 0.504 AC: 76641 AN: 152112 Hom.: 19883 Cov.: 33 AF XY: 0.508 AC XY: 37741 AN XY: 74354

African (AFR) AF: 0.614 AC: 25469 AN: 41508

American (AMR) AF: 0.580 AC: 8857 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1425 AN: 3466

East Asian (EAS) AF: 0.621 AC: 3213 AN: 5170

South Asian (SAS) AF: 0.531 AC: 2566 AN: 4830

European-Finnish (FIN) AF: 0.460 AC: 4860 AN: 10560

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.421 AC: 28643 AN: 67988

Other (OTH) AF: 0.506 AC: 1066 AN: 2108

Alfa AF: 0.420 Hom.: 6740

Bravo AF: 0.516

Asia WGS AF: 0.617 AC: 2144 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	0.25
DANN	Benign	0.47
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs869451; hg19: chr11-113753012;