Genetic Variant LINC02284:n.635+10168C>T (chr14-56355238-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 ENST00000560924.2(LINC02284):n.635+10168C>T variant causes a intron change. 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 0.033 ( 152 hom., cov: 9)

Consequence

LINC02284
ENST00000560924.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

No conservation score assigned

Publications

3 publications found

Variant links:

Genes affected

LINC02284 (HGNC:53201): (long intergenic non-protein coding RNA 2284)

LINC02284 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0781 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02284	NR_187174.1 link	n.620+10168C>T		intron_variant	Intron 6 of 6
LINC02284	NR_187175.1 link	n.582+10168C>T		intron_variant	Intron 5 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02284	ENST00000560924.2 link	n.635+10168C>T	intron_variant	Intron 5 of 6	4
LINC02284	ENST00000664388.1 link	n.665+10168C>T	intron_variant	Intron 6 of 6
LINC02284	ENST00000732419.1 link	n.574+10168C>T	intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.0326

AC:

2278

AN:

69946

Hom.:

151

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0670

Gnomad AMI

AF:

0.00380

Gnomad AMR

AF:

0.0705

Gnomad ASJ

AF:

0.0120

Gnomad EAS

AF:

0.0881

Gnomad SAS

AF:

0.0437

Gnomad FIN

AF:

0.0111

Gnomad MID

AF:

0.00847

Gnomad NFE

AF:

0.0120

Gnomad OTH

AF:

0.0323

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

GnomAD4 genome

AF:

0.0326

AC:

2279

AN:

69962

Hom.:

152

Cov.:

AF XY:

0.0343

AC XY:

1096

AN XY:

31992

show subpopulations

African (AFR)

AF:

0.0670

AC:

954

AN:

14230

American (AMR)

AF:

0.0703

AC:

453

AN:

6444

Ashkenazi Jewish (ASJ)

AF:

0.0120

AC:

AN:

1754

East Asian (EAS)

AF:

0.0876

AC:

221

AN:

2524

South Asian (SAS)

AF:

0.0432

AC:

107

AN:

2478

European-Finnish (FIN)

AF:

0.0111

AC:

AN:

2788

Middle Eastern (MID)

AF:

0.00893

AC:

AN:

112

European-Non Finnish (NFE)

AF:

0.0120

AC:

459

AN:

38236

Other (OTH)

AF:

0.0345

AC:

AN:

870

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.435

Heterozygous variant carriers

129

193

258

322

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

120

<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:

0.112

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.0

(source)

DANN

Benign

0.11

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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