11-113522272-C-T

Position:

• chr11-113522272-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 0.263 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.152

Gnomad4 AMR AF: 0.302

Gnomad4 ASJ AF: 0.432

Gnomad4 EAS AF: 0.0269

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.329

Alfa AF: 0.352 Hom.: 9260

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2514218; hg19: chr11-113392994;