Genetic Variant LINC00452:n.1111A>G (chr13-113919624-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000426859.1(LINC00452):n.1111A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,289,082 control chromosomes in the GnomAD database, including 26,097 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 ( 5131 hom., cov: 33)

Exomes 𝑓: 0.19 ( 20966 hom. )

Consequence

LINC00452
ENST00000426859.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.299

Publications

21 publications found

Variant links:

Genes affected

LINC00452 (HGNC:42800): (long intergenic non-protein coding RNA 452)

LINC00452 links:

ENSG00000293677 (HGNC:):

ENSG00000293677 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 (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00452	NR_164112.1 link	n.1111A>G		non_coding_transcript_exon_variant	Exon 6 of 8

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00452	ENST00000426859.1 link	n.1111A>G	non_coding_transcript_exon_variant	Exon 6 of 8	2
LINC00452	ENST00000671032.1 link	n.433A>G	non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000293677	ENST00000717691.1 link	n.688A>G	non_coding_transcript_exon_variant	Exon 4 of 7

Frequencies

GnomAD3 genomes

AF:

0.235

AC:

35755

AN:

151952

Hom.:

5104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.412

Gnomad AMR

AF:

0.189

Gnomad ASJ

AF:

0.238

Gnomad EAS

AF:

0.0495

Gnomad SAS

AF:

0.102

Gnomad FIN

AF:

0.102

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.190

Gnomad OTH

AF:

0.234

GnomAD2 exomes

AF:

0.166

AC:

22294

AN:

134502

AF XY:

0.162

show subpopulations

Gnomad AFR exome

AF:

0.404

Gnomad AMR exome

AF:

0.141

Gnomad ASJ exome

AF:

0.228

Gnomad EAS exome

AF:

0.0514

Gnomad FIN exome

AF:

0.106

Gnomad NFE exome

AF:

0.193

Gnomad OTH exome

AF:

0.181

GnomAD4 exome

AF:

0.186

AC:

211075

AN:

1137012

Hom.:

20966

Cov.:

AF XY:

0.182

AC XY:

101605

AN XY:

557718

show subpopulations

African (AFR)

AF:

0.407

AC:

9934

AN:

24394

American (AMR)

AF:

0.143

AC:

4030

AN:

28252

Ashkenazi Jewish (ASJ)

AF:

0.230

AC:

3672

AN:

15936

East Asian (EAS)

AF:

0.0512

AC:

656

AN:

12820

South Asian (SAS)

AF:

0.102

AC:

7791

AN:

76196

European-Finnish (FIN)

AF:

0.117

AC:

1530

AN:

13080

Middle Eastern (MID)

AF:

0.180

AC:

790

AN:

4394

European-Non Finnish (NFE)

AF:

0.190

AC:

174721

AN:

920426

Other (OTH)

AF:

0.192

AC:

7951

AN:

41514

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

8461

16922

25382

33843

42304

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7146

14292

21438

28584

35730

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.236

AC:

35839

AN:

152070

Hom.:

5131

Cov.:

AF XY:

0.228

AC XY:

16920

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.397

AC:

16456

AN:

41484

American (AMR)

AF:

0.189

AC:

2890

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.238

AC:

823

AN:

3464

East Asian (EAS)

AF:

0.0494

AC:

255

AN:

5162

South Asian (SAS)

AF:

0.102

AC:

493

AN:

4828

European-Finnish (FIN)

AF:

0.102

AC:

1082

AN:

10582

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.190

AC:

12919

AN:

67950

Other (OTH)

AF:

0.232

AC:

489

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1366

2732

4097

5463

6829

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

348

696

1044

1392

1740

<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:

0.209

Hom.:

11097

Bravo

AF:

0.253

Asia WGS

AF:

0.0870

AC:

305

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

2.3

(source)

DANN

Benign

0.34

PhyloP100

0.30

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over