ENST00000664116.1:n.872-9C>T

Variant names:

• chr11-15930748-C-T
• rs11023787
• ENST00000664116.1:n.872-9C>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000664116.1(LINC02682):​n.872-9C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0599 in 152,242 control chromosomes in the GnomAD database, including 868 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 0.060 (868 hom., cov: 32)
• Consequence: LINC02682 ENST00000664116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715

Genes affected

LINC02682 (HGNC:54177): (long intergenic non-protein coding RNA 2682)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02682	ENST00000664116.1	n.872-9C>T		intron_variant	Intron 8 of 8

Frequencies

GnomAD3 genomes AF: 0.0600 AC: 9124 AN: 152124 Hom.: 867 Cov.: 32

Gnomad AFR AF: 0.0186

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0733

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.0512

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0427

Gnomad OTH AF: 0.0707

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

GnomAD4 genome AF: 0.0599 AC: 9125 AN: 152242 Hom.: 868 Cov.: 32 AF XY: 0.0647 AC XY: 4814 AN XY: 74428

Gnomad4 AFR AF: 0.0186

Gnomad4 AMR AF: 0.0735

Gnomad4 ASJ AF: 0.0683

Gnomad4 EAS AF: 0.492

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0512

Gnomad4 NFE AF: 0.0427

Gnomad4 OTH AF: 0.0738

Alfa AF: 0.0688 Hom.: 1291

Bravo AF: 0.0611

Asia WGS AF: 0.285 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.75
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11023787; hg19: chr11-15952294;