Genetic Variant ENST00000599841.1:n.25-579_25-566delACACACACACACAC (chr16-86197744-CGTGTGTGTGTGTGT-C) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The ENST00000599841.1(ENSG00000268505):n.25-579_25-566delACACACACACACAC variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 0)

Consequence

ENSG00000268505
ENST00000599841.1 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.19

Publications

1 publications found

Variant links:

Genes affected

ENSG00000268505 (HGNC:):

ENSG00000268505 links:

LINC01082 (HGNC:49125): (long intergenic non-protein coding RNA 1082)

LINC01082 links:

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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
LINC01082	NR_103859.1 link	n.232+1349_232+1362delGTGTGTGTGTGTGT		intron_variant	Intron 1 of 1
LOC124903743	XR_007065164.1 link	n.628-579_628-566delACACACACACACAC		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000268505	ENST00000599841.1 link	n.25-579_25-566delACACACACACACAC	intron_variant	Intron 1 of 2	4
LINC01082	ENST00000601250.1 link	n.232+1333_232+1346delGTGTGTGTGTGTGT	intron_variant	Intron 1 of 1	2
LINC01082	ENST00000669926.3 link	n.508+1333_508+1346delGTGTGTGTGTGTGT	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

Cov.:

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

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over