11-113522272-C-T

Variant names:

• chr11-113522272-C-T
• rs2514218

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 0.263 in 152,058 control chromosomes in the GnomAD database, including 6,078 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 0.26 (6078 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 82 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 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: 0.264 AC: 40050 AN: 151940 Hom.: 6082 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.242

Gnomad AMR AF: 0.302

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.0274

Gnomad SAS AF: 0.238

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.395

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.263 AC: 40039 AN: 152058 Hom.: 6078 Cov.: 31 AF XY: 0.254 AC XY: 18866 AN XY: 74342

African (AFR) AF: 0.152 AC: 6325 AN: 41478

American (AMR) AF: 0.302 AC: 4614 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1498 AN: 3466

East Asian (EAS) AF: 0.0269 AC: 139 AN: 5168

South Asian (SAS) AF: 0.238 AC: 1144 AN: 4814

European-Finnish (FIN) AF: 0.172 AC: 1827 AN: 10596

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.345 AC: 23465 AN: 67932

Other (OTH) AF: 0.329 AC: 694 AN: 2112

Alfa AF: 0.333 Hom.: 22181

Bravo AF: 0.272

Asia WGS AF: 0.128 AC: 450 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.4
DANN	Benign	0.57
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2514218; hg19: chr11-113392994;