Genetic Variant LINC02226:n.262-23394A>G (chr5-8233238-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 ENST00000654773.1(LINC02226):n.262-23394A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,208 control chromosomes in the GnomAD database, including 2,373 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 0.16 ( 2373 hom., cov: 33)

Consequence

LINC02226
ENST00000654773.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.675

Publications

5 publications found

Variant links:

Genes affected

LINC02226 (HGNC:53095): (long intergenic non-protein coding RNA 2226)

LINC02226 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=-0.96).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02226	ENST00000654773.1 link	n.262-23394A>G	intron_variant	Intron 1 of 1
LINC02226	ENST00000847314.1 link	n.455+3929A>G	intron_variant	Intron 4 of 4
LINC02226	ENST00000847315.1 link	n.359-23394A>G	intron_variant	Intron 3 of 3
LINC02226	ENST00000847680.1 link	n.99+3929A>G	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24217

AN:

152090

Hom.:

2364

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0983

Gnomad AMI

AF:

0.231

Gnomad AMR

AF:

0.222

Gnomad ASJ

AF:

0.136

Gnomad EAS

AF:

0.408

Gnomad SAS

AF:

0.343

Gnomad FIN

AF:

0.155

Gnomad MID

AF:

0.218

Gnomad NFE

AF:

0.150

Gnomad OTH

AF:

0.192

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

GnomAD4 genome

AF:

0.159

AC:

24238

AN:

152208

Hom.:

2373

Cov.:

AF XY:

0.166

AC XY:

12322

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0983

AC:

4086

AN:

41546

American (AMR)

AF:

0.222

AC:

3393

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.136

AC:

471

AN:

3466

East Asian (EAS)

AF:

0.407

AC:

2102

AN:

5160

South Asian (SAS)

AF:

0.342

AC:

1651

AN:

4822

European-Finnish (FIN)

AF:

0.155

AC:

1647

AN:

10596

Middle Eastern (MID)

AF:

0.218

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.150

AC:

10196

AN:

68014

Other (OTH)

AF:

0.197

AC:

417

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

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

288

576

864

1152

1440

<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:

0.159

Hom.:

8693

Bravo

AF:

0.160

Asia WGS

AF:

0.344

AC:

1195

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

2.2

(source)

DANN

Benign

0.48

PhyloP100

-0.68

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