Genetic Variant LINC00690:n.468+1254_468+1255insA (chr3-16526577-T-TA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The ENST00000655456.1(LINC00690):n.468+1254_468+1255insA variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00058 ( 0 hom., cov: 0)

Consequence

LINC00690
ENST00000655456.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.140

Publications

1 publications found

Variant links:

Genes affected

LINC00690 (HGNC:44503): (long intergenic non-protein coding RNA 690)

LINC00690 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00690	ENST00000655456.1 link	n.468+1254_468+1255insA	intron_variant	Intron 1 of 4
LINC00690	ENST00000659804.1 link	n.543+1254_543+1255insA	intron_variant	Intron 1 of 2
LINC00690	ENST00000660552.1 link	n.500+1254_500+1255insA	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.000578

AC:

AN:

146932

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000524

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000270

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000394

Gnomad SAS

AF:

0.00129

Gnomad FIN

AF:

0.00117

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000558

Gnomad OTH

AF:

0.00199

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

GnomAD4 genome

AF:

0.000585

AC:

AN:

147022

Hom.:

Cov.:

AF XY:

0.000643

AC XY:

AN XY:

71562

show subpopulations

African (AFR)

AF:

0.000523

AC:

AN:

40172

American (AMR)

AF:

0.000270

AC:

AN:

14824

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3392

East Asian (EAS)

AF:

0.000593

AC:

AN:

5058

South Asian (SAS)

AF:

0.00130

AC:

AN:

4632

European-Finnish (FIN)

AF:

0.00117

AC:

AN:

9418

Middle Eastern (MID)

AF:

0.00

AC:

AN:

280

European-Non Finnish (NFE)

AF:

0.000558

AC:

AN:

66312

Other (OTH)

AF:

0.00197

AC:

AN:

2030

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.409

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.000161

Hom.:

303

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.14

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.

3-16526577-TAA-TAAA

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