Genetic Variant LINC02348:n.608T>C (chr15-101613601-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 ENST00000618724.3(LINC02348):n.608T>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 0.463 in 152,094 control chromosomes in the GnomAD database, including 16,812 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 0.46 ( 16798 hom., cov: 32)

Exomes 𝑓: 0.47 ( 14 hom. )

Consequence

LINC02348
ENST00000618724.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00300

Publications

3 publications found

Variant links:

COSMIC-nc: COSV61751269

Genes affected

LINC02348 (HGNC:53270): (long intergenic non-protein coding RNA 2348)

LINC02348 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.51 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02348	NR_147041.1 link	n.564T>C		non_coding_transcript_exon_variant	Exon 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02348	ENST00000618724.3 link	n.608T>C	non_coding_transcript_exon_variant	Exon 2 of 3	4
LINC02348	ENST00000655738.1 link	n.756T>C	non_coding_transcript_exon_variant	Exon 2 of 3
LINC02348	ENST00000740832.1 link	n.189+2407T>C	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.463

AC:

70305

AN:

151838

Hom.:

16773

Cov.:

show subpopulations

Gnomad AFR

AF:

0.516

Gnomad AMI

AF:

0.509

Gnomad AMR

AF:

0.336

Gnomad ASJ

AF:

0.308

Gnomad EAS

AF:

0.241

Gnomad SAS

AF:

0.415

Gnomad FIN

AF:

0.476

Gnomad MID

AF:

0.259

Gnomad NFE

AF:

0.487

Gnomad OTH

AF:

0.411

GnomAD4 exome

AF:

0.471

AC:

AN:

138

Hom.:

AF XY:

0.480

AC XY:

AN XY:

102

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.509

AC:

AN:

116

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.463

AC:

70373

AN:

151956

Hom.:

16798

Cov.:

AF XY:

0.460

AC XY:

34135

AN XY:

74258

show subpopulations

African (AFR)

AF:

0.516

AC:

21391

AN:

41442

American (AMR)

AF:

0.335

AC:

5121

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.308

AC:

1069

AN:

3468

East Asian (EAS)

AF:

0.241

AC:

1243

AN:

5162

South Asian (SAS)

AF:

0.414

AC:

1995

AN:

4816

European-Finnish (FIN)

AF:

0.476

AC:

5024

AN:

10546

Middle Eastern (MID)

AF:

0.269

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.487

AC:

33114

AN:

67928

Other (OTH)

AF:

0.415

AC:

875

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1941

3882

5824

7765

9706

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

642

1284

1926

2568

3210

<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:

0.451

Hom.:

5985

Bravo

AF:

0.448

Asia WGS

AF:

0.373

AC:

1297

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.4

(source)

DANN

Benign

0.46

PhyloP100

-0.0030

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