Genetic Variant LINC02882:n.64-11265T>G (chr12-74388897-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000548427.2(LINC02882):n.64-11265T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 151,968 control chromosomes in the GnomAD database, including 50,359 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 0.79 ( 50359 hom., cov: 30)

Consequence

LINC02882
ENST00000548427.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.939

Publications

2 publications found

Variant links:

Genes affected

LINC02882 (HGNC:54802): (long intergenic non-protein coding RNA 2882)

LINC02882 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=-1.03).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 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
LINC02882	ENST00000548427.2 link	n.64-11265T>G	intron_variant	Intron 1 of 10	6
LINC02882	ENST00000551726.2 link	n.192+13107T>G	intron_variant	Intron 2 of 6	4
LINC02882	ENST00000653134.1 link	n.234+13107T>G	intron_variant	Intron 2 of 8

Frequencies

GnomAD3 genomes

AF:

0.794

AC:

120635

AN:

151850

Hom.:

50341

Cov.:

show subpopulations

Gnomad AFR

AF:

0.511

Gnomad AMI

AF:

0.961

Gnomad AMR

AF:

0.773

Gnomad ASJ

AF:

0.914

Gnomad EAS

AF:

0.940

Gnomad SAS

AF:

0.937

Gnomad FIN

AF:

0.968

Gnomad MID

AF:

0.854

Gnomad NFE

AF:

0.914

Gnomad OTH

AF:

0.809

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

GnomAD4 genome

AF:

0.794

AC:

120699

AN:

151968

Hom.:

50359

Cov.:

AF XY:

0.800

AC XY:

59425

AN XY:

74278

show subpopulations

African (AFR)

AF:

0.512

AC:

21197

AN:

41414

American (AMR)

AF:

0.772

AC:

11781

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.914

AC:

3173

AN:

3470

East Asian (EAS)

AF:

0.939

AC:

4821

AN:

5132

South Asian (SAS)

AF:

0.937

AC:

4511

AN:

4814

European-Finnish (FIN)

AF:

0.968

AC:

10229

AN:

10564

Middle Eastern (MID)

AF:

0.864

AC:

254

AN:

294

European-Non Finnish (NFE)

AF:

0.914

AC:

62148

AN:

68004

Other (OTH)

AF:

0.811

AC:

1709

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1004

2008

3013

4017

5021

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

852

1704

2556

3408

4260

<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:

0.801

Hom.:

5380

Bravo

AF:

0.765

Asia WGS

AF:

0.907

AC:

3155

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.1

(source)

DANN

Benign

0.28

PhyloP100

-0.94

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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