Genetic Variant LINC02301:n.316-2323A>T (chr14-82704378-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000555150.6(LINC02301):n.316-2323A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.113 in 152,038 control chromosomes in the GnomAD database, including 1,255 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 0.11 ( 1255 hom., cov: 32)

Consequence

LINC02301
ENST00000555150.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.337

Publications

2 publications found

Variant links:

Genes affected

LINC02301 (HGNC:53220): (long intergenic non-protein coding RNA 2301)

LINC02301 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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02301	NR_146650.1 link	n.304-2323A>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02301	ENST00000555150.6 link	n.316-2323A>T	intron_variant	Intron 5 of 5	3
LINC02301	ENST00000662642.1 link	n.184+17009A>T	intron_variant	Intron 3 of 4
LINC02301	ENST00000841947.1 link	n.182+17009A>T	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.113

AC:

17149

AN:

151920

Hom.:

1253

Cov.:

show subpopulations

Gnomad AFR

AF:

0.140

Gnomad AMI

AF:

0.130

Gnomad AMR

AF:

0.139

Gnomad ASJ

AF:

0.0524

Gnomad EAS

AF:

0.358

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.0854

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0736

Gnomad OTH

AF:

0.116

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

GnomAD4 genome

AF:

0.113

AC:

17161

AN:

152038

Hom.:

1255

Cov.:

AF XY:

0.118

AC XY:

8750

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.140

AC:

5805

AN:

41460

American (AMR)

AF:

0.139

AC:

2123

AN:

15262

Ashkenazi Jewish (ASJ)

AF:

0.0524

AC:

182

AN:

3470

East Asian (EAS)

AF:

0.358

AC:

1840

AN:

5142

South Asian (SAS)

AF:

0.193

AC:

930

AN:

4816

European-Finnish (FIN)

AF:

0.0854

AC:

903

AN:

10576

Middle Eastern (MID)

AF:

0.0476

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0736

AC:

5004

AN:

67992

Other (OTH)

AF:

0.114

AC:

242

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

734

1469

2203

2938

3672

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

200

400

600

800

1000

<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:

0.0886

Hom.:

Bravo

AF:

0.118

Asia WGS

AF:

0.279

AC:

969

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.6

(source)

DANN

Benign

0.55

PhyloP100

0.34

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