rs11023787

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664116.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02682	ENST00000664116.1		n.872-9C>T		intron	N/A
	LINC02682	ENST00000757694.1		n.478-9C>T		intron	N/A
	LINC02682	ENST00000757695.1		n.291-9C>T		intron	N/A

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

African (AFR) AF: 0.0186 AC: 773 AN: 41562

American (AMR) AF: 0.0735 AC: 1124 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0683 AC: 237 AN: 3472

East Asian (EAS) AF: 0.492 AC: 2534 AN: 5148

South Asian (SAS) AF: 0.173 AC: 832 AN: 4808

European-Finnish (FIN) AF: 0.0512 AC: 543 AN: 10610

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0427 AC: 2905 AN: 68020

Other (OTH) AF: 0.0738 AC: 156 AN: 2114

Alfa AF: 0.0622 Hom.: 1515

Bravo AF: 0.0611

Asia WGS AF: 0.285 AC: 989 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.75
DANN	Benign	0.41
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs11023787; hg19: chr11-15952294;