Genetic Variant LINC02055:n.186-55543G>A (chr8-136106932-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000502901.6(LINC02055):n.186-55543G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,010 control chromosomes in the GnomAD database, including 20,065 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 0.50 ( 20065 hom., cov: 33)

Consequence

LINC02055
ENST00000502901.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.522

Publications

7 publications found

Variant links:

Genes affected

LINC02055 (HGNC:52895): (long intergenic non-protein coding RNA 2055)

LINC02055 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 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
LINC02055	ENST00000502901.6 link	n.186-55543G>A	intron_variant	Intron 1 of 3	4
LINC02055	ENST00000523150.1 link	n.330+17726G>A	intron_variant	Intron 2 of 4	5
LINC02055	ENST00000648077.2 link	n.283+17726G>A	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.505

AC:

76638

AN:

151892

Hom.:

20045

Cov.:

show subpopulations

Gnomad AFR

AF:

0.477

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.641

Gnomad ASJ

AF:

0.516

Gnomad EAS

AF:

0.862

Gnomad SAS

AF:

0.678

Gnomad FIN

AF:

0.473

Gnomad MID

AF:

0.484

Gnomad NFE

AF:

0.458

Gnomad OTH

AF:

0.514

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

GnomAD4 genome

AF:

0.505

AC:

76700

AN:

152010

Hom.:

20065

Cov.:

AF XY:

0.511

AC XY:

37954

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.477

AC:

19771

AN:

41448

American (AMR)

AF:

0.642

AC:

9791

AN:

15254

Ashkenazi Jewish (ASJ)

AF:

0.516

AC:

1793

AN:

3472

East Asian (EAS)

AF:

0.862

AC:

4453

AN:

5164

South Asian (SAS)

AF:

0.677

AC:

3275

AN:

4834

European-Finnish (FIN)

AF:

0.473

AC:

4993

AN:

10554

Middle Eastern (MID)

AF:

0.466

AC:

137

AN:

294

European-Non Finnish (NFE)

AF:

0.458

AC:

31101

AN:

67966

Other (OTH)

AF:

0.520

AC:

1098

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1962

3924

5887

7849

9811

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

692

1384

2076

2768

3460

<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:

0.475

Hom.:

22748

Bravo

AF:

0.516

Asia WGS

AF:

0.742

AC:

2581

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.77

(source)

DANN

Benign

0.63

PhyloP100

0.52

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