Genetic Variant LINC01339:n.188+5150C>A (chr5-90148138-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000813478.1(LINC01339):n.188+5150C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0513 in 152,276 control chromosomes in the GnomAD database, including 312 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 0.051 ( 312 hom., cov: 33)

Consequence

LINC01339
ENST00000813478.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.137

Publications

0 publications found

Variant links:

Genes affected

LINC01339 (HGNC:50549): (long intergenic non-protein coding RNA 1339)

LINC01339 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=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01339	ENST00000813478.1 link	n.188+5150C>A	intron_variant	Intron 2 of 4
LINC01339	ENST00000813481.1 link	n.248+5150C>A	intron_variant	Intron 3 of 6
LINC01339	ENST00000813482.1 link	n.191+5150C>A	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.0512

AC:

7788

AN:

152158

Hom.:

311

Cov.:

show subpopulations

Gnomad AFR

AF:

0.116

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0285

Gnomad ASJ

AF:

0.0228

Gnomad EAS

AF:

0.00404

Gnomad SAS

AF:

0.0576

Gnomad FIN

AF:

0.0322

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0255

Gnomad OTH

AF:

0.0431

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

GnomAD4 genome

AF:

0.0513

AC:

7810

AN:

152276

Hom.:

312

Cov.:

AF XY:

0.0510

AC XY:

3800

AN XY:

74472

show subpopulations

African (AFR)

AF:

0.116

AC:

4810

AN:

41538

American (AMR)

AF:

0.0286

AC:

437

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0228

AC:

AN:

3470

East Asian (EAS)

AF:

0.00405

AC:

AN:

5186

South Asian (SAS)

AF:

0.0572

AC:

276

AN:

4824

European-Finnish (FIN)

AF:

0.0322

AC:

342

AN:

10624

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0255

AC:

1733

AN:

68020

Other (OTH)

AF:

0.0469

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

361

723

1084

1446

1807

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

276

368

460

<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:

0.0166

Hom.:

Bravo

AF:

0.0528

Asia WGS

AF:

0.0460

AC:

160

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.7

(source)

DANN

Benign

0.30

PhyloP100

0.14

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