rs11023787

Positions:

• chr11-15930748-C-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 splice polypyrimidine tract, intron, non coding transcript 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 splice_polypyrimidine_tract, intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02682	ENST00000664116.1	n.872-9C>T		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

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;