Genetic Variant LINC02328:n.391-16252C>G (chr14-86144612-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000655493.1(LINC02328):n.391-16252C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0214 in 152,228 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 0.021 ( 123 hom., cov: 31)

Consequence

LINC02328
ENST00000655493.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0830

Publications

2 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

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02328	ENST00000655493.1 link	n.391-16252C>G	intron_variant	Intron 1 of 1
LINC02328	ENST00000668344.4 link	n.568-16252C>G	intron_variant	Intron 3 of 3
LINC02328	ENST00000752522.1 link	n.433-16252C>G	intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes

AF:

0.0213

AC:

3244

AN:

152110

Hom.:

122

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00396

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0751

Gnomad ASJ

AF:

0.00202

Gnomad EAS

AF:

0.118

Gnomad SAS

AF:

0.0412

Gnomad FIN

AF:

0.0353

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0104

Gnomad OTH

AF:

0.0148

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

GnomAD4 genome

AF:

0.0214

AC:

3260

AN:

152228

Hom.:

123

Cov.:

AF XY:

0.0243

AC XY:

1809

AN XY:

74426

show subpopulations

African (AFR)

AF:

0.00395

AC:

164

AN:

41554

American (AMR)

AF:

0.0753

AC:

1151

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.00202

AC:

AN:

3464

East Asian (EAS)

AF:

0.118

AC:

612

AN:

5180

South Asian (SAS)

AF:

0.0412

AC:

198

AN:

4804

European-Finnish (FIN)

AF:

0.0353

AC:

374

AN:

10608

Middle Eastern (MID)

AF:

0.00

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0104

AC:

709

AN:

68012

Other (OTH)

AF:

0.0198

AC:

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

155

309

464

618

773

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

168

210

<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:

0.00400

Hom.:

Bravo

AF:

0.0247

Asia WGS

AF:

0.0870

AC:

301

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.36

(source)

DANN

Benign

0.46

PhyloP100

-0.083

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