Genetic Variant LINC02050:n.250+45658G>C (chr3-80816613-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000811634.1(LINC02050):n.250+45658G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.247 in 152,084 control chromosomes in the GnomAD database, including 5,536 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 0.25 ( 5536 hom., cov: 31)

Consequence

LINC02050
ENST00000811634.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.123

Publications

10 publications found

Variant links:

Genes affected

LINC02050 (HGNC:52890): (long intergenic non-protein coding RNA 2050)

LINC02050 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=-0.71).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02050	ENST00000811634.1 link	n.250+45658G>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.247

AC:

37489

AN:

151966

Hom.:

5536

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0870

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.284

Gnomad ASJ

AF:

0.407

Gnomad EAS

AF:

0.134

Gnomad SAS

AF:

0.348

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.348

Gnomad NFE

AF:

0.319

Gnomad OTH

AF:

0.259

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

GnomAD4 genome

AF:

0.247

AC:

37498

AN:

152084

Hom.:

5536

Cov.:

AF XY:

0.248

AC XY:

18420

AN XY:

74312

show subpopulations

African (AFR)

AF:

0.0869

AC:

3607

AN:

41516

American (AMR)

AF:

0.284

AC:

4337

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.407

AC:

1413

AN:

3470

East Asian (EAS)

AF:

0.134

AC:

691

AN:

5152

South Asian (SAS)

AF:

0.349

AC:

1681

AN:

4818

European-Finnish (FIN)

AF:

0.295

AC:

3117

AN:

10578

Middle Eastern (MID)

AF:

0.347

AC:

102

AN:

294

European-Non Finnish (NFE)

AF:

0.320

AC:

21713

AN:

67954

Other (OTH)

AF:

0.260

AC:

549

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1354

2708

4062

5416

6770

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

402

804

1206

1608

2010

<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:

0.290

Hom.:

3691

Bravo

AF:

0.235

Asia WGS

AF:

0.230

AC:

796

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

(source)

DANN

Benign

0.94

PhyloP100

0.12

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