dbSNP rs10498602: LINC02328:n.183-990A>G (chr14-86126960-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 ENST00000553668.2(LINC02328):n.183-990A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0221 in 152,180 control chromosomes in the GnomAD database, including 123 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 0.022 ( 123 hom., cov: 32)

Consequence

LINC02328
ENST00000553668.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0690

Publications

0 publications found

Variant links:

Genes affected

LINC02328 (HGNC:53248): (long intergenic non-protein coding RNA 2328)

LINC02328 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02328	NR_110155.1 link	n.290-990A>G		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02328	ENST00000553668.2 link	n.183-990A>G	intron_variant	Intron 2 of 4	3
LINC02328	ENST00000557195.5 link	n.446-990A>G	intron_variant	Intron 4 of 4	3
LINC02328	ENST00000654590.3 link	n.395-990A>G	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.0220

AC:

3340

AN:

152062

Hom.:

122

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00618

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0752

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.0414

Gnomad FIN

AF:

0.0354

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.0153

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

GnomAD4 genome

AF:

0.0221

AC:

3358

AN:

152180

Hom.:

123

Cov.:

AF XY:

0.0249

AC XY:

1852

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.00621

AC:

258

AN:

41564

American (AMR)

AF:

0.0754

AC:

1152

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.00202

AC:

AN:

3468

East Asian (EAS)

AF:

0.118

AC:

609

AN:

5182

South Asian (SAS)

AF:

0.0414

AC:

200

AN:

4828

European-Finnish (FIN)

AF:

0.0354

AC:

375

AN:

10602

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0105

AC:

711

AN:

67942

Other (OTH)

AF:

0.0204

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

164

329

493

658

822

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

132

176

220

<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:

0.0156

Hom.:

Bravo

AF:

0.0254

Asia WGS

AF:

0.0870

AC:

302

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.69

(source)

DANN

Benign

0.39

PhyloP100

-0.069

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