dbSNP rs1673101: LINC02488:n.127-5559G>A (chr5-87738535-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 ENST00000815382.1(LINC02488):n.127-5559G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.315 in 151,822 control chromosomes in the GnomAD database, including 7,662 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 0.31 ( 7662 hom., cov: 32)

Consequence

LINC02488
ENST00000815382.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.442

Publications

3 publications found

Variant links:

Genes affected

LINC02488 (HGNC:53467): (long intergenic non-protein coding RNA 2488)

LINC02488 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=-0.67).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02488	ENST00000815382.1 link	n.127-5559G>A	intron_variant	Intron 1 of 6
LINC02488	ENST00000815383.1 link	n.127-5559G>A	intron_variant	Intron 1 of 5
LINC02488	ENST00000815384.1 link	n.97-5559G>A	intron_variant	Intron 1 of 5

Frequencies

GnomAD3 genomes

AF:

0.314

AC:

47694

AN:

151702

Hom.:

7633

Cov.:

show subpopulations

Gnomad AFR

AF:

0.327

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.318

Gnomad ASJ

AF:

0.321

Gnomad EAS

AF:

0.247

Gnomad SAS

AF:

0.202

Gnomad FIN

AF:

0.400

Gnomad MID

AF:

0.325

Gnomad NFE

AF:

0.305

Gnomad OTH

AF:

0.326

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

GnomAD4 genome

AF:

0.315

AC:

47772

AN:

151822

Hom.:

7662

Cov.:

AF XY:

0.318

AC XY:

23558

AN XY:

74158

show subpopulations

African (AFR)

AF:

0.328

AC:

13555

AN:

41384

American (AMR)

AF:

0.319

AC:

4864

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.321

AC:

1112

AN:

3464

East Asian (EAS)

AF:

0.247

AC:

1275

AN:

5158

South Asian (SAS)

AF:

0.202

AC:

969

AN:

4808

European-Finnish (FIN)

AF:

0.400

AC:

4218

AN:

10536

Middle Eastern (MID)

AF:

0.325

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.305

AC:

20704

AN:

67896

Other (OTH)

AF:

0.328

AC:

692

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1652

3304

4955

6607

8259

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

486

972

1458

1944

2430

<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:

0.310

Hom.:

4255

Bravo

AF:

0.312

Asia WGS

AF:

0.269

AC:

935

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

2.3

(source)

DANN

Benign

0.81

PhyloP100

-0.44

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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