Genetic Variant LINC02357:n.1408+3299G>A (chr4-26083889-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000637313.1(LINC02357):n.1408+3299G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,032 control chromosomes in the GnomAD database, including 5,888 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 0.27 ( 5888 hom., cov: 32)

Consequence

LINC02357
ENST00000637313.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.948

Publications

82 publications found

Variant links:

Genes affected

LINC02357 (HGNC:53279): (long intergenic non-protein coding RNA 2357)

LINC02357 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=-0.81).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.292 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02357	XR_925506.3 link	n.1408+3299G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02357	ENST00000637313.1 link	n.1408+3299G>A	intron_variant	Intron 2 of 2	5
LINC02357	ENST00000733074.1 link	n.407+3299G>A	intron_variant	Intron 2 of 2
LINC02357	ENST00000733075.1 link	n.371+3299G>A	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.270

AC:

40955

AN:

151914

Hom.:

5878

Cov.:

show subpopulations

Gnomad AFR

AF:

0.285

Gnomad AMI

AF:

0.325

Gnomad AMR

AF:

0.240

Gnomad ASJ

AF:

0.266

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.135

Gnomad FIN

AF:

0.273

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.296

Gnomad OTH

AF:

0.284

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

GnomAD4 genome

AF:

0.270

AC:

40986

AN:

152032

Hom.:

5888

Cov.:

AF XY:

0.264

AC XY:

19630

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.285

AC:

11810

AN:

41418

American (AMR)

AF:

0.239

AC:

3660

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.266

AC:

923

AN:

3470

East Asian (EAS)

AF:

0.00231

AC:

AN:

5186

South Asian (SAS)

AF:

0.135

AC:

653

AN:

4822

European-Finnish (FIN)

AF:

0.273

AC:

2880

AN:

10568

Middle Eastern (MID)

AF:

0.224

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.296

AC:

20095

AN:

67968

Other (OTH)

AF:

0.280

AC:

591

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1551

3101

4652

6202

7753

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

414

828

1242

1656

2070

<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:

0.284

Hom.:

31171

Bravo

AF:

0.270

Asia WGS

AF:

0.0760

AC:

268

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

(source)

DANN

Benign

0.71

PhyloP100

0.95

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