Genetic Variant LINC02386:n.547T>C (chr12-30200961-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000824537.1(LINC02386):n.547T>C 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 0.321 in 153,274 control chromosomes in the GnomAD database, including 11,897 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 0.32 ( 11873 hom., cov: 33)

Exomes 𝑓: 0.17 ( 24 hom. )

Consequence

LINC02386
ENST00000824537.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.121

Publications

1 publications found

Variant links:

Genes affected

LINC02386 (HGNC:53312): (long intergenic non-protein coding RNA 2386)

LINC02386 links:

ENSG00000257262 (HGNC:):

ENSG00000257262 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02386	ENST00000824537.1 link	n.547T>C	non_coding_transcript_exon_variant	Exon 1 of 2
LINC02386	ENST00000824538.1 link	n.154T>C	non_coding_transcript_exon_variant	Exon 1 of 2
LINC02386	ENST00000824524.1 link	n.170-1322T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.322

AC:

48913

AN:

151958

Hom.:

11857

Cov.:

show subpopulations

Gnomad AFR

AF:

0.659

Gnomad AMI

AF:

0.0285

Gnomad AMR

AF:

0.205

Gnomad ASJ

AF:

0.202

Gnomad EAS

AF:

0.637

Gnomad SAS

AF:

0.284

Gnomad FIN

AF:

0.224

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.273

GnomAD4 exome

AF:

0.170

AC:

204

AN:

1198

Hom.:

Cov.:

AF XY:

0.185

AC XY:

122

AN XY:

658

show subpopulations

African (AFR)

AF:

0.700

AC:

AN:

American (AMR)

AF:

0.167

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.107

AC:

AN:

East Asian (EAS)

AF:

0.750

AC:

AN:

South Asian (SAS)

AF:

0.206

AC:

AN:

European-Finnish (FIN)

AF:

0.182

AC:

AN:

Middle Eastern (MID)

AF:

0.167

AC:

AN:

European-Non Finnish (NFE)

AF:

0.141

AC:

129

AN:

916

Other (OTH)

AF:

0.154

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.530

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.322

AC:

48969

AN:

152076

Hom.:

11873

Cov.:

AF XY:

0.325

AC XY:

24180

AN XY:

74350

show subpopulations

African (AFR)

AF:

0.659

AC:

27337

AN:

41484

American (AMR)

AF:

0.205

AC:

3128

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.202

AC:

702

AN:

3468

East Asian (EAS)

AF:

0.638

AC:

3281

AN:

5146

South Asian (SAS)

AF:

0.283

AC:

1364

AN:

4822

European-Finnish (FIN)

AF:

0.224

AC:

2371

AN:

10584

Middle Eastern (MID)

AF:

0.259

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.149

AC:

10111

AN:

67968

Other (OTH)

AF:

0.272

AC:

573

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

1348

2697

4045

5394

6742

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

440

880

1320

1760

2200

<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:

0.215

Hom.:

1084

Bravo

AF:

0.334

Asia WGS

AF:

0.430

AC:

1495

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.5

(source)

DANN

Benign

0.40

PhyloP100

0.12

Mutation Taster

=100/0

polymorphism

(source)

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over