Genetic Variant LINC01389:n.29-6335delC (chr1-47416235-TG-T) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NR_126355.1(LINC01389):n.29-6335delC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00384 in 929,636 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00092 ( 0 hom., cov: 31)

Exomes 𝑓: 0.0044 ( 0 hom. )

Consequence

LINC01389
NR_126355.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.312

Variant links:

Genes affected

LINC01389 (HGNC:50661): (long intergenic non-protein coding RNA 1389)

LINC01389 links:

FOXE3 (HGNC:3808): (forkhead box E3) This intronless gene belongs to the forkhead family of transcription factors, which is characterized by a distinct forkhead domain. The protein encoded functions as a lens-specific transcription factor and plays an important role in vertebrate lens formation. Mutations in this gene are associated with anterior segment mesenchymal dysgenesis and congenital primary aphakia. [provided by RefSeq, Dec 2009]

FOXE3 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01389	NR_126355.1 link	n.29-6335delC		intron_variant	Intron 1 of 4
FOXE3	NM_012186.3 link	c.-80delG		upstream_gene_variant		ENST00000335071.4	NP_036318.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FOXE3	ENST00000335071.4 link	c.-80delG		upstream_gene_variant		6	NM_012186.3	ENSP00000334472.2		Q13461

Frequencies

GnomAD3 genomes

AF:

0.000919

AC:

131

AN:

142620

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00263

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000556

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000845

Gnomad SAS

AF:

0.000459

Gnomad FIN

AF:

0.000439

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000154

Gnomad OTH

AF:

0.000510

GnomAD4 exome

AF:

0.00437

AC:

3436

AN:

786946

Hom.:

Cov.:

AF XY:

0.00463

AC XY:

1740

AN XY:

376172

show subpopulations

Gnomad4 AFR exome

AF:

0.00624

Gnomad4 AMR exome

AF:

0.0107

Gnomad4 ASJ exome

AF:

0.00771

Gnomad4 EAS exome

AF:

0.00587

Gnomad4 SAS exome

AF:

0.00950

Gnomad4 FIN exome

AF:

0.00901

Gnomad4 NFE exome

AF:

0.00392

Gnomad4 OTH exome

AF:

0.00511

GnomAD4 genome

AF:

0.000918

AC:

131

AN:

142690

Hom.:

Cov.:

AF XY:

0.000878

AC XY:

AN XY:

69474

show subpopulations

Gnomad4 AFR

AF:

0.00262

Gnomad4 AMR

AF:

0.000555

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000849

Gnomad4 SAS

AF:

0.000460

Gnomad4 FIN

AF:

0.000439

Gnomad4 NFE

AF:

0.000155

Gnomad4 OTH

AF:

0.000505

Bravo

AF:

0.000971

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

1-47416235-TGGGGG-TGGGG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over