dbSNP rs2137476: LINC02089:n.680-1874C>T (chr17-53103164-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000715801.1(LINC02089):n.680-1874C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,996 control chromosomes in the GnomAD database, including 41,819 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 0.70 ( 41819 hom., cov: 31)

Consequence

LINC02089
ENST00000715801.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.73

Publications

0 publications found

Variant links:

Genes affected

LINC02089 (HGNC:52940): (long intergenic non-protein coding RNA 2089)

LINC02089 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=-0.93).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 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
LINC02089	ENST00000715801.1 link	n.680-1874C>T		intron_variant	Intron 4 of 4
LINC02089	ENST00000741187.1 link	n.120-1874C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.701

AC:

106422

AN:

151878

Hom.:

41809

Cov.:

show subpopulations

Gnomad AFR

AF:

0.307

Gnomad AMI

AF:

0.916

Gnomad AMR

AF:

0.821

Gnomad ASJ

AF:

0.853

Gnomad EAS

AF:

0.743

Gnomad SAS

AF:

0.845

Gnomad FIN

AF:

0.877

Gnomad MID

AF:

0.787

Gnomad NFE

AF:

0.859

Gnomad OTH

AF:

0.752

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

GnomAD4 genome

AF:

0.700

AC:

106447

AN:

151996

Hom.:

41819

Cov.:

AF XY:

0.705

AC XY:

52376

AN XY:

74272

show subpopulations

African (AFR)

AF:

0.307

AC:

12737

AN:

41452

American (AMR)

AF:

0.821

AC:

12538

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.853

AC:

2961

AN:

3472

East Asian (EAS)

AF:

0.744

AC:

3808

AN:

5120

South Asian (SAS)

AF:

0.844

AC:

4059

AN:

4808

European-Finnish (FIN)

AF:

0.877

AC:

9301

AN:

10604

Middle Eastern (MID)

AF:

0.781

AC:

228

AN:

292

European-Non Finnish (NFE)

AF:

0.859

AC:

58399

AN:

67962

Other (OTH)

AF:

0.749

AC:

1581

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1156

2313

3469

4626

5782

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

788

1576

2364

3152

3940

<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:

0.789

Hom.:

19305

Bravo

AF:

0.678

Asia WGS

AF:

0.766

AC:

2660

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.10

(source)

DANN

Benign

0.47

PhyloP100

-1.7

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