chr11-56480601-A-C

Position:

• chr11-56480601-A-C

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 0.118 in 152,254 control chromosomes in the GnomAD database, including 1,165 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 0.12 (1165 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.56480601A>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000290753	ENST00000641241.1	n.67-139T>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.118 AC: 18001 AN: 152134 Hom.: 1165 Cov.: 33

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0982

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.144

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0946

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

GnomAD4 genome AF: 0.118 AC: 18005 AN: 152254 Hom.: 1165 Cov.: 33 AF XY: 0.122 AC XY: 9053 AN XY: 74424

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.0979

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.144

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.0926

Alfa AF: 0.0763 Hom.: 114

Bravo AF: 0.111

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.7
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs637249; hg19: chr11-56248077;