Genetic Variant LINC02718:n.624+102397T>A (chr11-23023046-T-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NR_187205.1(LINC02718):n.624+102397T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,058 control chromosomes in the GnomAD database, including 5,174 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 0.25 ( 5174 hom., cov: 32)

Consequence

LINC02718
NR_187205.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.621

Publications

9 publications found

Variant links:

Genes affected

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

LINC02718 links:

LOC124902646 (HGNC:):

LOC124902646 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02718	NR_187205.1 link	n.624+102397T>A	intron_variant	Intron 4 of 13
LINC02718	NR_187206.1 link	n.624+102397T>A	intron_variant	Intron 4 of 11
LINC02718	NR_187207.1 link	n.624+102397T>A	intron_variant	Intron 4 of 12

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.253

AC:

38462

AN:

151940

Hom.:

5168

Cov.:

show subpopulations

Gnomad AFR

AF:

0.283

Gnomad AMI

AF:

0.154

Gnomad AMR

AF:

0.315

Gnomad ASJ

AF:

0.309

Gnomad EAS

AF:

0.356

Gnomad SAS

AF:

0.393

Gnomad FIN

AF:

0.143

Gnomad MID

AF:

0.347

Gnomad NFE

AF:

0.218

Gnomad OTH

AF:

0.276

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

GnomAD4 genome

AF:

0.253

AC:

38490

AN:

152058

Hom.:

5174

Cov.:

AF XY:

0.253

AC XY:

18780

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.283

AC:

11735

AN:

41480

American (AMR)

AF:

0.315

AC:

4814

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.309

AC:

1072

AN:

3466

East Asian (EAS)

AF:

0.355

AC:

1829

AN:

5148

South Asian (SAS)

AF:

0.393

AC:

1893

AN:

4816

European-Finnish (FIN)

AF:

0.143

AC:

1514

AN:

10590

Middle Eastern (MID)

AF:

0.342

AC:

100

AN:

292

European-Non Finnish (NFE)

AF:

0.218

AC:

14815

AN:

67964

Other (OTH)

AF:

0.273

AC:

578

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1441

2882

4324

5765

7206

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

404

808

1212

1616

2020

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.227

Hom.:

484

Bravo

AF:

0.263

Asia WGS

AF:

0.348

AC:

1209

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.48

(source)

DANN

Benign

0.34

PhyloP100

-0.62

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over