11-56474785-G-T

Position:

• chr11-56474785-G-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 0.111 in 152,072 control chromosomes in the GnomAD database, including 1,067 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 0.11 (1067 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.112 AC: 16944 AN: 151954 Hom.: 1069 Cov.: 32

Gnomad AFR AF: 0.0804

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0955

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.143

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.198

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.0909

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

GnomAD4 genome AF: 0.111 AC: 16934 AN: 152072 Hom.: 1067 Cov.: 32 AF XY: 0.115 AC XY: 8511 AN XY: 74296

Gnomad4 AFR AF: 0.0803

Gnomad4 AMR AF: 0.0952

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.143

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.198

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.0890

Alfa AF: 0.104 Hom.: 456

Bravo AF: 0.104

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.5
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7939886; hg19: chr11-56242261;