chr16-86197744-C-CGTGTGTGTGTGT

Variant names:

• chr16-86197744-C-CGTGTGTGTGTGT
• rs58016760
• ENST00000599841.1:n.25-566_25-565insACACACACACAC

Variant summary

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

The ENST00000599841.1(ENSG00000268505):​n.25-566_25-565insACACACACACAC 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 INS_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: 𝑓 0.000014 (0 hom., cov: 0)
• Consequence: ENSG00000268505 ENST00000599841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 1 publications found

Genes affected

ENSG00000268505 (HGNC:):

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

ACMG classification

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	n.232+1351_232+1362dupGTGTGTGTGTGT		intron_variant	Intron 1 of 1
LOC124903743	XR_007065164.1	n.628-577_628-566dupACACACACACAC		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268505	ENST00000599841.1	n.25-566_25-565insACACACACACAC		intron_variant	Intron 1 of 2	4
LINC01082	ENST00000601250.1	n.232+1332_232+1333insGTGTGTGTGTGT		intron_variant	Intron 1 of 1	2
LINC01082	ENST00000669926.3	n.508+1332_508+1333insGTGTGTGTGTGT		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0000135 AC: 2 AN: 147856 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.0000505

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000135 AC: 2 AN: 147856 Hom.: 0 Cov.: 0 AF XY: 0.0000278 AC XY: 2 AN XY: 71866

African (AFR) AF: 0.0000505 AC: 2 AN: 39626

American (AMR) AF: 0.00 AC: 0 AN: 14950

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3430

East Asian (EAS) AF: 0.00 AC: 0 AN: 4988

South Asian (SAS) AF: 0.00 AC: 0 AN: 4566

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9950

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 314

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67122

Other (OTH) AF: 0.00 AC: 0 AN: 2010

Alfa AF: 0.00 Hom.: 76

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs58016760; hg19: chr16-86231350;