Genetic Variant LINC02450:n.490+9902T>C (chr12-42717888-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 ENST00000761458.1(LINC02450):n.490+9902T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,064 control chromosomes in the GnomAD database, including 4,728 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 0.24 ( 4728 hom., cov: 32)

Consequence

LINC02450
ENST00000761458.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.158

Publications

2 publications found

Variant links:

Genes affected

LINC02450 (HGNC:53382): (long intergenic non-protein coding RNA 2450)

LINC02450 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=-0.83).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02450	ENST00000761458.1 link	n.490+9902T>C	intron_variant	Intron 2 of 2
LINC02450	ENST00000761459.1 link	n.255-18087T>C	intron_variant	Intron 2 of 2
LINC02450	ENST00000761462.1 link	n.41+9902T>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.240

AC:

36461

AN:

151946

Hom.:

4725

Cov.:

show subpopulations

Gnomad AFR

AF:

0.201

Gnomad AMI

AF:

0.199

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.226

Gnomad EAS

AF:

0.00445

Gnomad SAS

AF:

0.228

Gnomad FIN

AF:

0.240

Gnomad MID

AF:

0.222

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.244

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

GnomAD4 genome

AF:

0.240

AC:

36483

AN:

152064

Hom.:

4728

Cov.:

AF XY:

0.233

AC XY:

17309

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.201

AC:

8338

AN:

41504

American (AMR)

AF:

0.174

AC:

2658

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.226

AC:

783

AN:

3466

East Asian (EAS)

AF:

0.00446

AC:

AN:

5160

South Asian (SAS)

AF:

0.229

AC:

1104

AN:

4826

European-Finnish (FIN)

AF:

0.240

AC:

2534

AN:

10572

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.299

AC:

20284

AN:

67940

Other (OTH)

AF:

0.242

AC:

511

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1409

2818

4226

5635

7044

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

386

772

1158

1544

1930

<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:

0.267

Hom.:

7247

Bravo

AF:

0.231

Asia WGS

AF:

0.110

AC:

384

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

1.8

(source)

DANN

Benign

0.79

PhyloP100

-0.16

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