Genetic Variant LINC02113:n.521+8958C>T (chr5-99445399-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000510302.2(LINC02113):n.521+8958C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 151,936 control chromosomes in the GnomAD database, including 12,039 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 0.39 ( 12039 hom., cov: 32)

Consequence

LINC02113
ENST00000510302.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.116

Publications

9 publications found

Variant links:

Genes affected

LINC02113 (HGNC:52967): (long intergenic non-protein coding RNA 2113)

LINC02113 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=-1.0).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.417 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
LINC02113	ENST00000510302.2 link	n.521+8958C>T	intron_variant	Intron 2 of 5	3
LINC02113	ENST00000844080.1 link	n.417+34537C>T	intron_variant	Intron 1 of 2
LINC02113	ENST00000844081.1 link	n.518+34537C>T	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.394

AC:

59772

AN:

151818

Hom.:

12020

Cov.:

show subpopulations

Gnomad AFR

AF:

0.320

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.409

Gnomad ASJ

AF:

0.362

Gnomad EAS

AF:

0.386

Gnomad SAS

AF:

0.366

Gnomad FIN

AF:

0.515

Gnomad MID

AF:

0.341

Gnomad NFE

AF:

0.421

Gnomad OTH

AF:

0.402

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

GnomAD4 genome

AF:

0.394

AC:

59833

AN:

151936

Hom.:

12039

Cov.:

AF XY:

0.397

AC XY:

29481

AN XY:

74250

show subpopulations

African (AFR)

AF:

0.320

AC:

13253

AN:

41448

American (AMR)

AF:

0.409

AC:

6245

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.362

AC:

1255

AN:

3470

East Asian (EAS)

AF:

0.386

AC:

1997

AN:

5168

South Asian (SAS)

AF:

0.366

AC:

1763

AN:

4814

European-Finnish (FIN)

AF:

0.515

AC:

5434

AN:

10560

Middle Eastern (MID)

AF:

0.342

AC:

100

AN:

292

European-Non Finnish (NFE)

AF:

0.421

AC:

28583

AN:

67910

Other (OTH)

AF:

0.404

AC:

849

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1854

3709

5563

7418

9272

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

572

1144

1716

2288

2860

<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:

0.405

Hom.:

28647

Bravo

AF:

0.383

Asia WGS

AF:

0.366

AC:

1277

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.0

(source)

DANN

Benign

0.35

PhyloP100

0.12

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