dbSNP rs1491148: LINC02466:n.354+15659A>G (chr4-129708851-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000653915.1(LINC02466):n.354+15659A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0573 in 152,190 control chromosomes in the GnomAD database, including 737 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 0.057 ( 737 hom., cov: 32)

Consequence

LINC02466
ENST00000653915.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.305

Publications

1 publications found

Variant links:

Genes affected

LINC02466 (HGNC:53405): (long intergenic non-protein coding RNA 2466)

LINC02466 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=-0.87).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02466	ENST00000653915.1 link	n.354+15659A>G	intron_variant	Intron 4 of 4
LINC02466	ENST00000654715.1 link	n.558-12501A>G	intron_variant	Intron 5 of 7
LINC02466	ENST00000665329.1 link	n.280-12501A>G	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.0572

AC:

8697

AN:

152074

Hom.:

734

Cov.:

show subpopulations

Gnomad AFR

AF:

0.179

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0233

Gnomad ASJ

AF:

0.00375

Gnomad EAS

AF:

0.0711

Gnomad SAS

AF:

0.0629

Gnomad FIN

AF:

0.000659

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.00205

Gnomad OTH

AF:

0.0464

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

GnomAD4 genome

AF:

0.0573

AC:

8724

AN:

152190

Hom.:

737

Cov.:

AF XY:

0.0573

AC XY:

4265

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.179

AC:

7418

AN:

41542

American (AMR)

AF:

0.0233

AC:

356

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.00375

AC:

AN:

3468

East Asian (EAS)

AF:

0.0717

AC:

372

AN:

5190

South Asian (SAS)

AF:

0.0632

AC:

305

AN:

4826

European-Finnish (FIN)

AF:

0.000659

AC:

AN:

10630

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00205

AC:

139

AN:

67942

Other (OTH)

AF:

0.0507

AC:

107

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

376

751

1127

1502

1878

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

276

368

460

<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:

0.0342

Hom.:

Bravo

AF:

0.0641

Asia WGS

AF:

0.100

AC:

345

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

6.0

(source)

DANN

Benign

0.76

PhyloP100

0.30

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