Genetic Variant ENST00000502160.6:n.2447+300C>T (chr12-108448086-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 ENST00000502160.6(LINC01498):n.2447+300C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,090 control chromosomes in the GnomAD database, including 2,372 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 0.14 ( 2372 hom., cov: 32)

Consequence

LINC01498
ENST00000502160.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.539

Publications

8 publications found

Variant links:

Genes affected

LINC01498 (HGNC:51164): (long intergenic non-protein coding RNA 1498)

LINC01498 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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01498	ENST00000502160.6 link	n.2447+300C>T	intron_variant	Intron 13 of 17	5
LINC01498	ENST00000732921.1 link	n.506+300C>T	intron_variant	Intron 4 of 4
LINC01498	ENST00000732922.1 link	n.451+300C>T	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.141

AC:

21408

AN:

151972

Hom.:

2362

Cov.:

show subpopulations

Gnomad AFR

AF:

0.166

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.310

Gnomad ASJ

AF:

0.131

Gnomad EAS

AF:

0.482

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.104

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.0693

Gnomad OTH

AF:

0.154

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

GnomAD4 genome

AF:

0.141

AC:

21458

AN:

152090

Hom.:

2372

Cov.:

AF XY:

0.149

AC XY:

11094

AN XY:

74348

show subpopulations

African (AFR)

AF:

0.166

AC:

6904

AN:

41470

American (AMR)

AF:

0.311

AC:

4741

AN:

15264

Ashkenazi Jewish (ASJ)

AF:

0.131

AC:

455

AN:

3472

East Asian (EAS)

AF:

0.482

AC:

2489

AN:

5164

South Asian (SAS)

AF:

0.136

AC:

656

AN:

4816

European-Finnish (FIN)

AF:

0.104

AC:

1105

AN:

10576

Middle Eastern (MID)

AF:

0.163

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0693

AC:

4712

AN:

68010

Other (OTH)

AF:

0.154

AC:

325

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

829

1658

2488

3317

4146

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

222

444

666

888

1110

<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:

0.106

Hom.:

4285

Bravo

AF:

0.162

Asia WGS

AF:

0.264

AC:

917

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.80

(source)

DANN

Benign

0.28

PhyloP100

-0.54

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