11-23202402-C-T

Variant names:

• chr11-23202402-C-T
• rs1600958
• ENST00000533591.1:n.522-596C>T

Variant summary

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

The NR_187205.1(LINC02718):​n.1656-596C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,188 control chromosomes in the GnomAD database, including 25,981 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 0.58 (25981 hom., cov: 34)
• Consequence: LINC02718 NR_187205.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290

Genes affected

LINC02718 (HGNC:54235): (long intergenic non-protein coding RNA 2718)

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 = 0.965 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02718	NR_187205.1	n.1656-596C>T		intron_variant	Intron 13 of 13
LINC02718	NR_187206.1	n.1380-596C>T		intron_variant	Intron 11 of 11
LINC02718	NR_187207.1	n.1483-2114C>T		intron_variant	Intron 12 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02718	ENST00000533591.1	n.522-596C>T		intron_variant	Intron 6 of 6	5

Frequencies

GnomAD3 genomes AF: 0.576 AC: 87563 AN: 152070 Hom.: 25966 Cov.: 34

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.446

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.579

Gnomad EAS AF: 0.988

Gnomad SAS AF: 0.691

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.585

Gnomad OTH AF: 0.570

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

GnomAD4 genome AF: 0.576 AC: 87617 AN: 152188 Hom.: 25981 Cov.: 34 AF XY: 0.581 AC XY: 43199 AN XY: 74406

Gnomad4 AFR AF: 0.480

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.579

Gnomad4 EAS AF: 0.988

Gnomad4 SAS AF: 0.691

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.585

Gnomad4 OTH AF: 0.573

Alfa AF: 0.567 Hom.: 3091

Bravo AF: 0.576

Asia WGS AF: 0.812 AC: 2824 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	5.8
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1600958; hg19: chr11-23223948;