dbSNP rs10988341: LINC01503:n.420-2558A>G (chr9-129352900-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000423122.2(LINC01503):n.420-2558A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0352 in 151,972 control chromosomes in the GnomAD database, including 166 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 0.035 ( 166 hom., cov: 32)

Consequence

LINC01503
ENST00000423122.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.54

Publications

3 publications found

Variant links:

Genes affected

LINC01503 (HGNC:51184): (long intergenic non-protein coding RNA 1503)

LINC01503 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.148 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
LINC01503	ENST00000423122.2 link	n.420-2558A>G	intron_variant	Intron 1 of 2	2
LINC01503	ENST00000657393.1 link	n.658-2558A>G	intron_variant	Intron 2 of 3
LINC01503	ENST00000657651.2 link	n.557-2558A>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.0352

AC:

5348

AN:

151854

Hom.:

165

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00832

Gnomad AMI

AF:

0.00879

Gnomad AMR

AF:

0.0244

Gnomad ASJ

AF:

0.0418

Gnomad EAS

AF:

0.157

Gnomad SAS

AF:

0.0942

Gnomad FIN

AF:

0.0286

Gnomad MID

AF:

0.0510

Gnomad NFE

AF:

0.0415

Gnomad OTH

AF:

0.0360

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

GnomAD4 genome

AF:

0.0352

AC:

5345

AN:

151972

Hom.:

166

Cov.:

AF XY:

0.0361

AC XY:

2682

AN XY:

74274

show subpopulations

African (AFR)

AF:

0.00830

AC:

344

AN:

41454

American (AMR)

AF:

0.0244

AC:

372

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.0418

AC:

145

AN:

3470

East Asian (EAS)

AF:

0.157

AC:

808

AN:

5142

South Asian (SAS)

AF:

0.0943

AC:

454

AN:

4816

European-Finnish (FIN)

AF:

0.0286

AC:

302

AN:

10556

Middle Eastern (MID)

AF:

0.0445

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0415

AC:

2823

AN:

67952

Other (OTH)

AF:

0.0361

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

257

515

772

1030

1287

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

222

296

370

<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:

0.0376

Hom.:

273

Bravo

AF:

0.0325

Asia WGS

AF:

0.109

AC:

379

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

6.8

(source)

DANN

Benign

0.49

PhyloP100

-1.5

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