Genetic Variant LINC02253:n.88-8893C>A (chr15-97227328-C-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000559321.2(LINC02253):n.88-8893C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 151,944 control chromosomes in the GnomAD database, including 3,476 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 0.21 ( 3476 hom., cov: 32)

Consequence

LINC02253
ENST00000559321.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.12

Publications

0 publications found

Variant links:

Genes affected

LINC02253 (HGNC:53151): (long intergenic non-protein coding RNA 2253)

LINC02253 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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 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
LINC02253	ENST00000559321.2 link	n.88-8893C>A	intron_variant	Intron 1 of 5	2
LINC02253	ENST00000669885.1 link	n.190+2611C>A	intron_variant	Intron 1 of 5
LINC02253	ENST00000740177.1 link	n.390-8893C>A	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.209

AC:

31699

AN:

151826

Hom.:

3460

Cov.:

show subpopulations

Gnomad AFR

AF:

0.193

Gnomad AMI

AF:

0.181

Gnomad AMR

AF:

0.254

Gnomad ASJ

AF:

0.217

Gnomad EAS

AF:

0.375

Gnomad SAS

AF:

0.208

Gnomad FIN

AF:

0.226

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.193

Gnomad OTH

AF:

0.202

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

GnomAD4 genome

AF:

0.209

AC:

31749

AN:

151944

Hom.:

3476

Cov.:

AF XY:

0.210

AC XY:

15627

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.193

AC:

8011

AN:

41444

American (AMR)

AF:

0.254

AC:

3868

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.217

AC:

752

AN:

3472

East Asian (EAS)

AF:

0.376

AC:

1937

AN:

5150

South Asian (SAS)

AF:

0.208

AC:

1003

AN:

4820

European-Finnish (FIN)

AF:

0.226

AC:

2382

AN:

10548

Middle Eastern (MID)

AF:

0.177

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.193

AC:

13138

AN:

67946

Other (OTH)

AF:

0.209

AC:

442

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1224

2447

3671

4894

6118

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

340

680

1020

1360

1700

<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:

0.123

Hom.:

296

Bravo

AF:

0.217

Asia WGS

AF:

0.301

AC:

1048

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

0.83

(source)

DANN

Benign

0.64

PhyloP100

-1.1

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