dbSNP rs396250: LINC01492:n.-20C>T (chr9-103325054-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 ENST00000411575.5(LINC01492):n.-20C>T variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0863 in 152,188 control chromosomes in the GnomAD database, including 665 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 0.086 ( 665 hom., cov: 32)

Failed GnomAD Quality Control

Consequence

LINC01492
ENST00000411575.5 upstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.966

Publications

1 publications found

Variant links:

Genes affected

LINC01492 (HGNC:51149): (long intergenic non-protein coding RNA 1492)

LINC01492 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=-0.96).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.106 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01492	NR_121578.1 link	n.-21C>T		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
LINC01492	ENST00000411575.5 link	n.-20C>T	upstream_gene_variant	1
LINC01492	ENST00000806271.1 link	n.-4C>T	upstream_gene_variant
LINC01492	ENST00000806272.1 link	n.-9C>T	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.0864

AC:

13142

AN:

152070

Hom.:

665

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0580

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.0896

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.0154

Gnomad SAS

AF:

0.110

Gnomad FIN

AF:

0.0524

Gnomad MID

AF:

0.174

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.110

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.0863

AC:

13135

AN:

152188

Hom.:

665

Cov.:

AF XY:

0.0849

AC XY:

6318

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0578

AC:

2399

AN:

41510

American (AMR)

AF:

0.0895

AC:

1367

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.138

AC:

478

AN:

3472

East Asian (EAS)

AF:

0.0155

AC:

AN:

5178

South Asian (SAS)

AF:

0.111

AC:

535

AN:

4822

European-Finnish (FIN)

AF:

0.0524

AC:

555

AN:

10586

Middle Eastern (MID)

AF:

0.173

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.108

AC:

7345

AN:

68018

Other (OTH)

AF:

0.109

AC:

230

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

606

1212

1818

2424

3030

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

152

304

456

608

760

<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:

0.0895

Hom.:

Bravo

AF:

0.0872

Asia WGS

AF:

0.0530

AC:

182

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

4.8

(source)

DANN

Benign

0.35

PhyloP100

0.97

Mutation Taster

=100/0

polymorphism

(source)

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