11-23202402-C-T

Variant names:

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

Variant summary

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

The ENST00000533591.1(LINC02718):​n.522-596C>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 ENST00000533591.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.290
• Publications: 1 publications found

Genes affected

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

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 = 0.965 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000533591.1. 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
	LINC02718	NR_187205.1		n.1656-596C>T		intron	N/A
	LINC02718	NR_187206.1		n.1380-596C>T		intron	N/A
	LINC02718	NR_187207.1		n.1483-2114C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02718	ENST00000533591.1	TSL:5	n.522-596C>T		intron	N/A

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

African (AFR) AF: 0.480 AC: 19938 AN: 41508

American (AMR) AF: 0.621 AC: 9502 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.579 AC: 2012 AN: 3472

East Asian (EAS) AF: 0.988 AC: 5098 AN: 5160

South Asian (SAS) AF: 0.691 AC: 3335 AN: 4828

European-Finnish (FIN) AF: 0.586 AC: 6210 AN: 10600

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.585 AC: 39753 AN: 68000

Other (OTH) AF: 0.573 AC: 1210 AN: 2112

Alfa AF: 0.564 Hom.: 3183

Bravo AF: 0.576

Asia WGS AF: 0.812 AC: 2824 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	5.8
DANN	Benign	0.48
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs1600958; hg19: chr11-23223948;