11-56254458-C-T

Variant names:

• chr11-56254458-C-T
• rs1481928

Variant summary

Our verdict is Benign. The variant received -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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.321
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.715 AC: 29658 AN: 41460

American (AMR) AF: 0.700 AC: 10665 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2001 AN: 3458

East Asian (EAS) AF: 0.832 AC: 4287 AN: 5150

South Asian (SAS) AF: 0.797 AC: 3831 AN: 4804

European-Finnish (FIN) AF: 0.761 AC: 8032 AN: 10550

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 44955 AN: 67784

Other (OTH) AF: 0.691 AC: 1456 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.10
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs1481928; hg19: chr11-56021934;