11-13253006-A-T

Position:

• chr11-13253006-A-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 0.656 in 151,842 control chromosomes in the GnomAD database, including 33,224 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 0.66 (33224 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.413

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.13253006A>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99461 AN: 151724 Hom.: 33174 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.604

Gnomad AMR AF: 0.652

Gnomad ASJ AF: 0.714

Gnomad EAS AF: 0.496

Gnomad SAS AF: 0.648

Gnomad FIN AF: 0.741

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.656 AC: 99569 AN: 151842 Hom.: 33224 Cov.: 31 AF XY: 0.657 AC XY: 48796 AN XY: 74224

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.652

Gnomad4 ASJ AF: 0.714

Gnomad4 EAS AF: 0.496

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.741

Gnomad4 NFE AF: 0.723

Gnomad4 OTH AF: 0.676

Alfa AF: 0.687 Hom.: 4257

Bravo AF: 0.646

Asia WGS AF: 0.585 AC: 2035 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs747601; hg19: chr11-13274553;