Genetic Variant LINC01496:n.1346G>A (chrX-51498820-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000656579.1(LINC01496):n.1346G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.66 ( 16963 hom., 21374 hem., cov: 22)

Failed GnomAD Quality Control

Consequence

LINC01496
ENST00000656579.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.542

Publications

119 publications found

Variant links:

Genes affected

LINC01496 (HGNC:51162): (long intergenic non-protein coding RNA 1496)

LINC01496 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01496	ENST00000656579.1 link	n.1346G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LINC01496	ENST00000827922.1 link	n.*240G>A		downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.657

AC:

72368

AN:

110204

Hom.:

16965

Cov.:

show subpopulations

Gnomad AFR

AF:

0.623

Gnomad AMI

AF:

0.582

Gnomad AMR

AF:

0.784

Gnomad ASJ

AF:

0.748

Gnomad EAS

AF:

0.922

Gnomad SAS

AF:

0.724

Gnomad FIN

AF:

0.564

Gnomad MID

AF:

0.678

Gnomad NFE

AF:

0.636

Gnomad OTH

AF:

0.670

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

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.656

AC:

72383

AN:

110256

Hom.:

16963

Cov.:

AF XY:

0.657

AC XY:

21374

AN XY:

32522

show subpopulations

African (AFR)

AF:

0.623

AC:

18865

AN:

30299

American (AMR)

AF:

0.785

AC:

8195

AN:

10442

Ashkenazi Jewish (ASJ)

AF:

0.748

AC:

1973

AN:

2638

East Asian (EAS)

AF:

0.922

AC:

3197

AN:

3466

South Asian (SAS)

AF:

0.722

AC:

1801

AN:

2496

European-Finnish (FIN)

AF:

0.564

AC:

3307

AN:

5860

Middle Eastern (MID)

AF:

0.665

AC:

141

AN:

212

European-Non Finnish (NFE)

AF:

0.636

AC:

33500

AN:

52668

Other (OTH)

AF:

0.674

AC:

1017

AN:

1510

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

912

1825

2737

3650

4562

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

640

1280

1920

2560

3200

<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:

0.646

Hom.:

65996

Bravo

AF:

0.674

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.94

(source)

DANN

Benign

0.43

PhyloP100

-0.54

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