11-133697090-C-T

Variant names:

• chr11-133697090-C-T
• rs4397868
• ENST00000762255.1:n.378+28277G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000762255.1(LINC02743):​n.378+28277G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,244 control chromosomes in the GnomAD database, including 58,176 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 0.87 (58176 hom., cov: 32)
• Consequence: LINC02743 ENST00000762255.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 15 publications found

Genes affected

LINC02743 (HGNC:54261): (long intergenic non-protein coding RNA 2743)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000762255.1. You can select a different transcript below to see updated ACMG assignments.

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
	LINC02743	ENST00000762255.1		n.378+28277G>A		intron	N/A
	LINC02743	ENST00000762256.1		n.388+28277G>A		intron	N/A
	LINC02743	ENST00000762257.1		n.402+28277G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132526 AN: 152126 Hom.: 58115 Cov.: 32

Gnomad AFR AF: 0.963

Gnomad AMI AF: 0.744

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.922

Gnomad FIN AF: 0.815

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.885

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

GnomAD4 genome AF: 0.871 AC: 132647 AN: 152244 Hom.: 58176 Cov.: 32 AF XY: 0.872 AC XY: 64932 AN XY: 74426

African (AFR) AF: 0.963 AC: 40038 AN: 41558

American (AMR) AF: 0.904 AC: 13831 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3012 AN: 3470

East Asian (EAS) AF: 0.937 AC: 4849 AN: 5176

South Asian (SAS) AF: 0.922 AC: 4452 AN: 4828

European-Finnish (FIN) AF: 0.815 AC: 8636 AN: 10592

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.809 AC: 55005 AN: 68006

Other (OTH) AF: 0.886 AC: 1873 AN: 2114

Alfa AF: 0.840 Hom.: 175141

Bravo AF: 0.881

Asia WGS AF: 0.942 AC: 3276 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.078
DANN	Benign	0.64
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4397868; hg19: chr11-133566985;