Genetic Variant LINC02519:n.207+8198T>C (chr6-169380003-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 ENST00000440168.1(LINC02519):n.186-4226T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.869 in 152,308 control chromosomes in the GnomAD database, including 57,714 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 0.87 ( 57714 hom., cov: 34)

Consequence

LINC02519
ENST00000440168.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.02

Variant links:

Genes affected

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

LINC02519 links:

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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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02519	NR_187217.1 link	n.206+8198T>C		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02519	ENST00000433388.7 link	n.207+8198T>C	intron_variant	Intron 1 of 1	3
LINC02519	ENST00000440168.1 link	n.186-4226T>C	intron_variant	Intron 1 of 1	2
LINC02519	ENST00000809422.1 link	n.176+8198T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.869

AC:

132299

AN:

152190

Hom.:

57663

Cov.:

show subpopulations

Gnomad AFR

AF:

0.906

Gnomad AMI

AF:

0.853

Gnomad AMR

AF:

0.893

Gnomad ASJ

AF:

0.849

Gnomad EAS

AF:

0.963

Gnomad SAS

AF:

0.940

Gnomad FIN

AF:

0.866

Gnomad MID

AF:

0.842

Gnomad NFE

AF:

0.831

Gnomad OTH

AF:

0.864

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

GnomAD4 genome

AF:

0.869

AC:

132411

AN:

152308

Hom.:

57714

Cov.:

AF XY:

0.874

AC XY:

65085

AN XY:

74474

show subpopulations

African (AFR)

AF:

0.906

AC:

37656

AN:

41564

American (AMR)

AF:

0.893

AC:

13668

AN:

15308

Ashkenazi Jewish (ASJ)

AF:

0.849

AC:

2949

AN:

3472

East Asian (EAS)

AF:

0.964

AC:

4991

AN:

5178

South Asian (SAS)

AF:

0.940

AC:

4542

AN:

4830

European-Finnish (FIN)

AF:

0.866

AC:

9193

AN:

10616

Middle Eastern (MID)

AF:

0.837

AC:

246

AN:

294

European-Non Finnish (NFE)

AF:

0.831

AC:

56563

AN:

68026

Other (OTH)

AF:

0.866

AC:

1827

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

915

1829

2744

3658

4573

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.855

Hom.:

7207

Bravo

AF:

0.871

Asia WGS

AF:

0.947

AC:

3293

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.044

(source)

DANN

Benign

0.60

PhyloP100

-2.0

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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6-169380003-A-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over