Genetic Variant LINC01013:n.309+2798_309+2799insTAAAA (chr6-131954052-T-TTAAAA) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000435287.2(LINC01013):n.309+2798_309+2799insTAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.54 ( 22555 hom., cov: 0)

Consequence

LINC01013
ENST00000435287.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0280

Publications

2 publications found

Variant links:

Genes affected

LINC01013 (HGNC:48987): (long intergenic non-protein coding RNA 1013)

LINC01013 links:

CCN2-AS1 (HGNC:40164): (CCN2 antisense RNA 1)

CCN2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -8 ACMG points.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.689 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000435287.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
CCN2-AS1	NR_187593.1	n.371+43098_371+43102dupTAAAA	intron	N/A
CCN2-AS1	NR_187594.1	n.488+49819_488+49823dupTAAAA	intron	N/A
CCN2-AS1	NR_187595.1	n.327+29983_327+29987dupTAAAA	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC01013	ENST00000435287.2	TSL:2	n.309+2798_309+2799insTAAAA	intron	N/A
LINC01013	ENST00000440246.2	TSL:3	n.96+3846_96+3847insTAAAA	intron	N/A
LINC01013	ENST00000706294.2		n.182+51901_182+51902insTAAAA	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.538

AC:

81270

AN:

151176

Hom.:

22512

Cov.:

show subpopulations

Gnomad AFR

AF:

0.695

Gnomad AMI

AF:

0.564

Gnomad AMR

AF:

0.485

Gnomad ASJ

AF:

0.396

Gnomad EAS

AF:

0.522

Gnomad SAS

AF:

0.497

Gnomad FIN

AF:

0.463

Gnomad MID

AF:

0.558

Gnomad NFE

AF:

0.477

Gnomad OTH

AF:

0.526

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

GnomAD4 genome

AF:

0.538

AC:

81367

AN:

151296

Hom.:

22555

Cov.:

AF XY:

0.535

AC XY:

39540

AN XY:

73896

show subpopulations

African (AFR)

AF:

0.695

AC:

28626

AN:

41162

American (AMR)

AF:

0.485

AC:

7382

AN:

15236

Ashkenazi Jewish (ASJ)

AF:

0.396

AC:

1370

AN:

3456

East Asian (EAS)

AF:

0.522

AC:

2676

AN:

5126

South Asian (SAS)

AF:

0.498

AC:

2393

AN:

4808

European-Finnish (FIN)

AF:

0.463

AC:

4820

AN:

10402

Middle Eastern (MID)

AF:

0.563

AC:

162

AN:

288

European-Non Finnish (NFE)

AF:

0.477

AC:

32310

AN:

67802

Other (OTH)

AF:

0.529

AC:

1116

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1820

3640

5460

7280

9100

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

692

1384

2076

2768

3460

<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:

0.495

Hom.:

2028

Asia WGS

AF:

0.560

AC:

1944

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.028

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over