Genetic Variant LINC02393:n.459C>T (chr12-127897105-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000614177.2(LINC02393):n.459C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.215 in 152,168 control chromosomes in the GnomAD database, including 5,302 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 0.21 ( 5302 hom., cov: 33)

Exomes 𝑓: 0.18 ( 0 hom. )

Consequence

LINC02393
ENST00000614177.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.146

Publications

4 publications found

Variant links:

Genes affected

LINC02393 (HGNC:53320): (long intergenic non-protein coding RNA 2393)

LINC02393 links:

LINC00508 (HGNC:43559): (long intergenic non-protein coding RNA 508)

LINC00508 links:

Genome browser will be placed here

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=-0.89).

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 rank	MANE	Protein	UniProt
LINC02393	NR_033987.1 link	n.486C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC00508	NR_126452.2 link	n.312-12000G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02393	ENST00000614177.2 link	n.459C>T	non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC02393	ENST00000662498.1 link	n.393C>T	non_coding_transcript_exon_variant	Exon 2 of 2
LINC00508	ENST00000741352.1 link	n.317-35249G>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.215

AC:

32639

AN:

152016

Hom.:

5298

Cov.:

show subpopulations

Gnomad AFR

AF:

0.438

Gnomad AMI

AF:

0.101

Gnomad AMR

AF:

0.138

Gnomad ASJ

AF:

0.0571

Gnomad EAS

AF:

0.493

Gnomad SAS

AF:

0.0902

Gnomad FIN

AF:

0.138

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.106

Gnomad OTH

AF:

0.191

GnomAD4 exome

AF:

0.176

AC:

AN:

Hom.:

Cov.:

AF XY:

0.182

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.143

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.517

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.215

AC:

32672

AN:

152134

Hom.:

5302

Cov.:

AF XY:

0.214

AC XY:

15904

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.438

AC:

18178

AN:

41474

American (AMR)

AF:

0.138

AC:

2108

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.0571

AC:

198

AN:

3470

East Asian (EAS)

AF:

0.492

AC:

2537

AN:

5152

South Asian (SAS)

AF:

0.0892

AC:

431

AN:

4830

European-Finnish (FIN)

AF:

0.138

AC:

1464

AN:

10582

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.106

AC:

7223

AN:

68020

Other (OTH)

AF:

0.188

AC:

398

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1155

2310

3464

4619

5774

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

314

628

942

1256

1570

<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:

0.165

Hom.:

1399

Bravo

AF:

0.228

Asia WGS

AF:

0.294

AC:

1023

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.9

(source)

DANN

Benign

0.56

PhyloP100

0.15

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