Genetic Variant LINC02882:n.1128-3438T>G (chr12-74296512-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.1128-3438T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,240 control chromosomes in the GnomAD database, including 1,047 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 0.11 ( 1047 hom., cov: 33)

Consequence

LINC02882
ENST00000548427.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.122

Publications

5 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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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.1128-3438T>G	intron_variant	Intron 10 of 10	6
LINC02882	ENST00000551726.2 link	n.464+10046T>G	intron_variant	Intron 4 of 6	4
LINC02882	ENST00000653134.1 link	n.477+10046T>G	intron_variant	Intron 4 of 8

Frequencies

GnomAD3 genomes

AF:

0.107

AC:

16352

AN:

152122

Hom.:

1048

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.0647

Gnomad AMR

AF:

0.0761

Gnomad ASJ

AF:

0.0981

Gnomad EAS

AF:

0.0969

Gnomad SAS

AF:

0.148

Gnomad FIN

AF:

0.0712

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0767

Gnomad OTH

AF:

0.0976

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

GnomAD4 genome

AF:

0.107

AC:

16358

AN:

152240

Hom.:

1047

Cov.:

AF XY:

0.108

AC XY:

8043

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.177

AC:

7369

AN:

41526

American (AMR)

AF:

0.0760

AC:

1162

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.0981

AC:

340

AN:

3466

East Asian (EAS)

AF:

0.0973

AC:

505

AN:

5188

South Asian (SAS)

AF:

0.147

AC:

712

AN:

4834

European-Finnish (FIN)

AF:

0.0712

AC:

756

AN:

10614

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0767

AC:

5215

AN:

67996

Other (OTH)

AF:

0.0966

AC:

204

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

745

1491

2236

2982

3727

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

186

372

558

744

930

<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:

0.0846

Hom.:

1059

Bravo

AF:

0.109

Asia WGS

AF:

0.0970

AC:

337

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

6.8

(source)

DANN

Benign

0.68

PhyloP100

-0.12

Mutation Taster

=100/0

polymorphism (auto)

(source)

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