dbSNP rs10498602: LINC02328:n.183-990A>G (chr14-86126960-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is . 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:

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new If you want to explore the variant's impact on the transcript ENST00000553668.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553668.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02328	NR_110155.1		n.290-990A>G		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC02328	ENST00000553668.2	TSL:3	n.183-990A>G	intron	N/A
LINC02328	ENST00000557195.5	TSL:3	n.446-990A>G	intron	N/A
LINC02328	ENST00000654590.3		n.395-990A>G	intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over