Genetic Variant LINC02395:n.406+4000C>T (chr12-49906641-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 ENST00000547954.2(LINC02395):n.406+4000C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.745 in 152,050 control chromosomes in the GnomAD database, including 42,801 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 0.75 ( 42801 hom., cov: 31)

Consequence

LINC02395
ENST00000547954.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.347

Publications

9 publications found

Variant links:

Genes affected

LINC02395 (HGNC:53322): (long intergenic non-protein coding RNA 2395)

LINC02395 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=-0.78).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02395	ENST00000547954.2 link	n.406+4000C>T	intron_variant	Intron 2 of 6	3
LINC02395	ENST00000551539.2 link	n.48+2638C>T	intron_variant	Intron 1 of 5	4
LINC02395	ENST00000655869.1 link	n.405+4000C>T	intron_variant	Intron 2 of 9

Frequencies

GnomAD3 genomes

AF:

0.745

AC:

113210

AN:

151932

Hom.:

42779

Cov.:

show subpopulations

Gnomad AFR

AF:

0.733

Gnomad AMI

AF:

0.806

Gnomad AMR

AF:

0.677

Gnomad ASJ

AF:

0.898

Gnomad EAS

AF:

0.371

Gnomad SAS

AF:

0.843

Gnomad FIN

AF:

0.727

Gnomad MID

AF:

0.839

Gnomad NFE

AF:

0.783

Gnomad OTH

AF:

0.762

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

GnomAD4 genome

AF:

0.745

AC:

113285

AN:

152050

Hom.:

42801

Cov.:

AF XY:

0.741

AC XY:

55079

AN XY:

74316

show subpopulations

African (AFR)

AF:

0.733

AC:

30361

AN:

41448

American (AMR)

AF:

0.676

AC:

10331

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.898

AC:

3119

AN:

3472

East Asian (EAS)

AF:

0.371

AC:

1917

AN:

5172

South Asian (SAS)

AF:

0.844

AC:

4069

AN:

4822

European-Finnish (FIN)

AF:

0.727

AC:

7675

AN:

10564

Middle Eastern (MID)

AF:

0.837

AC:

246

AN:

294

European-Non Finnish (NFE)

AF:

0.783

AC:

53227

AN:

67984

Other (OTH)

AF:

0.761

AC:

1608

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1431

2862

4292

5723

7154

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

844

1688

2532

3376

4220

<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:

0.771

Hom.:

166667

Bravo

AF:

0.735

Asia WGS

AF:

0.686

AC:

2389

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

6.7

(source)

DANN

Benign

0.85

PhyloP100

-0.35

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