Genetic Variant LINC02091:n.389-1876A>G (chr17-189133-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 ENST00000576171.1(LINC02091):n.389-1876A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 152,056 control chromosomes in the GnomAD database, including 28,600 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 0.61 ( 28600 hom., cov: 33)

Consequence

LINC02091
ENST00000576171.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.122

Publications

11 publications found

Variant links:

Genes affected

LINC02091 (HGNC:52942): (long intergenic non-protein coding RNA 2091)

LINC02091 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=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.813 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
LINC02091	ENST00000576171.1 link	n.389-1876A>G	intron_variant	Intron 1 of 2	5
LINC02091	ENST00000792641.1 link	n.407-1876A>G	intron_variant	Intron 1 of 2
LINC02091	ENST00000792642.1 link	n.512-1876A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.608

AC:

92379

AN:

151938

Hom.:

28579

Cov.:

show subpopulations

Gnomad AFR

AF:

0.516

Gnomad AMI

AF:

0.577

Gnomad AMR

AF:

0.704

Gnomad ASJ

AF:

0.576

Gnomad EAS

AF:

0.834

Gnomad SAS

AF:

0.675

Gnomad FIN

AF:

0.661

Gnomad MID

AF:

0.538

Gnomad NFE

AF:

0.614

Gnomad OTH

AF:

0.612

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

GnomAD4 genome

AF:

0.608

AC:

92441

AN:

152056

Hom.:

28600

Cov.:

AF XY:

0.613

AC XY:

45533

AN XY:

74302

show subpopulations

African (AFR)

AF:

0.516

AC:

21406

AN:

41468

American (AMR)

AF:

0.705

AC:

10765

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.576

AC:

1999

AN:

3468

East Asian (EAS)

AF:

0.834

AC:

4322

AN:

5182

South Asian (SAS)

AF:

0.675

AC:

3252

AN:

4818

European-Finnish (FIN)

AF:

0.661

AC:

6980

AN:

10558

Middle Eastern (MID)

AF:

0.527

AC:

155

AN:

294

European-Non Finnish (NFE)

AF:

0.614

AC:

41747

AN:

67974

Other (OTH)

AF:

0.613

AC:

1289

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1867

3734

5600

7467

9334

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

780

1560

2340

3120

3900

<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:

0.609

Hom.:

40162

Bravo

AF:

0.608

Asia WGS

AF:

0.730

AC:

2538

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.7

(source)

DANN

Benign

0.84

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