Genetic Variant LINC02519:n.207+7683A>G (chr6-169380518-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000433388.7(LINC02519):n.207+7683A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.305 in 152,126 control chromosomes in the GnomAD database, including 9,942 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 0.31 ( 9942 hom., cov: 33)

Consequence

LINC02519
ENST00000433388.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.853

Publications

2 publications found

Variant links:

Genes affected

LINC02519 (HGNC:53510): (long intergenic non-protein coding RNA 2519)

LINC02519 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02519	NR_187217.1 link	n.206+7683A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02519	ENST00000433388.7 link	n.207+7683A>G	intron_variant	Intron 1 of 1	3
LINC02519	ENST00000440168.1 link	n.186-4741A>G	intron_variant	Intron 1 of 1	2
LINC02519	ENST00000809422.1 link	n.176+7683A>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.305

AC:

46367

AN:

152010

Hom.:

9918

Cov.:

show subpopulations

Gnomad AFR

AF:

0.568

Gnomad AMI

AF:

0.112

Gnomad AMR

AF:

0.336

Gnomad ASJ

AF:

0.181

Gnomad EAS

AF:

0.611

Gnomad SAS

AF:

0.258

Gnomad FIN

AF:

0.189

Gnomad MID

AF:

0.209

Gnomad NFE

AF:

0.147

Gnomad OTH

AF:

0.271

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

GnomAD4 genome

AF:

0.305

AC:

46447

AN:

152126

Hom.:

9942

Cov.:

AF XY:

0.308

AC XY:

22919

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.568

AC:

23539

AN:

41472

American (AMR)

AF:

0.337

AC:

5155

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.181

AC:

629

AN:

3470

East Asian (EAS)

AF:

0.611

AC:

3158

AN:

5168

South Asian (SAS)

AF:

0.260

AC:

1251

AN:

4816

European-Finnish (FIN)

AF:

0.189

AC:

2000

AN:

10586

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.147

AC:

9984

AN:

68010

Other (OTH)

AF:

0.268

AC:

566

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1378

2756

4133

5511

6889

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

422

844

1266

1688

2110

<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:

0.234

Hom.:

2459

Bravo

AF:

0.329

Asia WGS

AF:

0.387

AC:

1343

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.9

(source)

DANN

Benign

0.84

PhyloP100

0.85

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