11-56254458-C-T

Position:

• chr11-56254458-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 0.696 in 151,758 control chromosomes in the GnomAD database, including 36,927 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 0.70 (36927 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.812 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.56254458C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.695 AC: 105444 AN: 151638 Hom.: 36879 Cov.: 33

Gnomad AFR AF: 0.715

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.832

Gnomad SAS AF: 0.799

Gnomad FIN AF: 0.761

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.696 AC: 105550 AN: 151758 Hom.: 36927 Cov.: 33 AF XY: 0.702 AC XY: 52078 AN XY: 74158

Gnomad4 AFR AF: 0.715

Gnomad4 AMR AF: 0.700

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.832

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.761

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.691

Alfa AF: 0.676 Hom.: 4350

Bravo AF: 0.689

Asia WGS AF: 0.826 AC: 2841 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.10

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1481928; hg19: chr11-56021934;