Genetic Variant LINC02822:n.860+51194G>A (chr12-90731139-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000652014.1(LINC02822):n.860+51194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,058 control chromosomes in the GnomAD database, including 1,704 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 0.15 ( 1704 hom., cov: 32)

Consequence

LINC02822
ENST00000652014.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.106

Publications

2 publications found

Variant links:

Genes affected

LINC02822 (HGNC:54353): (long intergenic non-protein coding RNA 2822)

LINC02822 links:

ENSG00000288102 (HGNC:):

ENSG00000288102 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=-0.9).

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
LINC02822	ENST00000652014.1 link	n.860+51194G>A	intron_variant	Intron 5 of 5
LINC02822	ENST00000664727.1 link	n.121+54527G>A	intron_variant	Intron 2 of 5
LINC02822	ENST00000666236.1 link	n.198+54488G>A	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22057

AN:

151940

Hom.:

1702

Cov.:

show subpopulations

Gnomad AFR

AF:

0.178

Gnomad AMI

AF:

0.0559

Gnomad AMR

AF:

0.0999

Gnomad ASJ

AF:

0.114

Gnomad EAS

AF:

0.0158

Gnomad SAS

AF:

0.119

Gnomad FIN

AF:

0.142

Gnomad MID

AF:

0.111

Gnomad NFE

AF:

0.151

Gnomad OTH

AF:

0.130

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

GnomAD4 genome

AF:

0.145

AC:

22087

AN:

152058

Hom.:

1704

Cov.:

AF XY:

0.142

AC XY:

10559

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.178

AC:

7374

AN:

41474

American (AMR)

AF:

0.0997

AC:

1523

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.114

AC:

396

AN:

3464

East Asian (EAS)

AF:

0.0157

AC:

AN:

5172

South Asian (SAS)

AF:

0.119

AC:

573

AN:

4830

European-Finnish (FIN)

AF:

0.142

AC:

1503

AN:

10574

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.151

AC:

10276

AN:

67956

Other (OTH)

AF:

0.131

AC:

276

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1001

2002

3002

4003

5004

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

246

492

738

984

1230

<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:

0.148

Hom.:

5467

Bravo

AF:

0.143

Asia WGS

AF:

0.0970

AC:

339

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.3

(source)

DANN

Benign

0.64

PhyloP100

0.11

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