chr11-13224675-T-G

Position:

• chr11-13224675-T-G

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 0.346 in 152,086 control chromosomes in the GnomAD database, including 11,205 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 0.35 (11205 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.594

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.13224675T>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52580 AN: 151966 Hom.: 11201 Cov.: 32

Gnomad AFR AF: 0.0919

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.492

Gnomad EAS AF: 0.348

Gnomad SAS AF: 0.474

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.439

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.386

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

GnomAD4 genome AF: 0.346 AC: 52592 AN: 152086 Hom.: 11205 Cov.: 32 AF XY: 0.350 AC XY: 26012 AN XY: 74324

Gnomad4 AFR AF: 0.0918

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.492

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.475

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.465

Gnomad4 OTH AF: 0.392

Alfa AF: 0.452 Hom.: 31114

Bravo AF: 0.321

Asia WGS AF: 0.389 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12808129; hg19: chr11-13246222;