11-54825685-C-T

Position:

• chr11-54825685-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 0.679 in 151,472 control chromosomes in the GnomAD database, including 35,508 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 0.68 (35508 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.761 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.54825685C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.679 AC: 102783 AN: 151354 Hom.: 35485 Cov.: 33

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.772

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.767

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.679 AC: 102848 AN: 151472 Hom.: 35508 Cov.: 33 AF XY: 0.678 AC XY: 50206 AN XY: 73998

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.772

Gnomad4 ASJ AF: 0.800

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.771

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.711

Gnomad4 OTH AF: 0.717

Alfa AF: 0.714 Hom.: 26145

Bravo AF: 0.682

Asia WGS AF: 0.769 AC: 2674 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1580785; hg19: chr11-51293595;