Genetic Variant LINC02513:n.235-32618T>G (chr4-38334253-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000503465.2(LINC02513):n.235-32618T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0458 in 152,270 control chromosomes in the GnomAD database, including 715 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 0.046 ( 715 hom., cov: 32)

Consequence

LINC02513
ENST00000503465.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.412

Publications

1 publications found

Variant links:

Genes affected

LINC02513 (HGNC:53502): (long intergenic non-protein coding RNA 2513)

LINC02513 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=-0.86).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 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
LINC02513	ENST00000503465.2 link	n.235-32618T>G	intron_variant	Intron 2 of 3	2
LINC02513	ENST00000757609.1 link	n.235-32618T>G	intron_variant	Intron 2 of 4
LINC02513	ENST00000757610.1 link	n.216-32618T>G	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0459

AC:

6981

AN:

152152

Hom.:

720

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00992

Gnomad AMI

AF:

0.0175

Gnomad AMR

AF:

0.114

Gnomad ASJ

AF:

0.00951

Gnomad EAS

AF:

0.454

Gnomad SAS

AF:

0.0668

Gnomad FIN

AF:

0.0325

Gnomad MID

AF:

0.0222

Gnomad NFE

AF:

0.0245

Gnomad OTH

AF:

0.0445

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

GnomAD4 genome

AF:

0.0458

AC:

6970

AN:

152270

Hom.:

715

Cov.:

AF XY:

0.0502

AC XY:

3739

AN XY:

74446

show subpopulations

African (AFR)

AF:

0.00989

AC:

411

AN:

41568

American (AMR)

AF:

0.114

AC:

1738

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.00951

AC:

AN:

3470

East Asian (EAS)

AF:

0.453

AC:

2346

AN:

5178

South Asian (SAS)

AF:

0.0660

AC:

318

AN:

4816

European-Finnish (FIN)

AF:

0.0325

AC:

345

AN:

10624

Middle Eastern (MID)

AF:

0.0204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0245

AC:

1663

AN:

68002

Other (OTH)

AF:

0.0445

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

287

574

862

1149

1436

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

160

240

320

400

<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:

0.0169

Hom.:

Bravo

AF:

0.0543

Asia WGS

AF:

0.204

AC:

707

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

5.9

(source)

DANN

Benign

0.66

PhyloP100

0.41

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