ENST00000599841.1:n.25-566_25-565insACACAC

Variant names:

• chr16-86197744-C-CGTGTGT
• rs58016760
• ENST00000599841.1:n.25-566_25-565insACACAC

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BS1 BS2

The ENST00000599841.1(ENSG00000268505):​n.25-566_25-565insACACAC 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 0.015 (36 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: Benign. The variant received -8 ACMG points.

• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0149 (2198/147954) while in subpopulation AFR AF = 0.0329 (1306/39738). AF 95% confidence interval is 0.0314. There are 36 homozygotes in GnomAd4. There are 1225 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 36 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01082	NR_103859.1	n.232+1357_232+1362dupGTGTGT		intron_variant	Intron 1 of 1
LOC124903743	XR_007065164.1	n.628-571_628-566dupACACAC		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_25-565insACACAC		intron_variant	Intron 1 of 2	4
LINC01082	ENST00000601250.1	n.232+1332_232+1333insGTGTGT		intron_variant	Intron 1 of 1	2
LINC01082	ENST00000669926.3	n.508+1332_508+1333insGTGTGT		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0149 AC: 2197 AN: 147848 Hom.: 36 Cov.: 0

Gnomad AFR AF: 0.0329

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00448

Gnomad ASJ AF: 0.00262

Gnomad EAS AF: 0.0138

Gnomad SAS AF: 0.00350

Gnomad FIN AF: 0.0595

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.00176

Gnomad OTH AF: 0.00995

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

GnomAD4 genome AF: 0.0149 AC: 2198 AN: 147954 Hom.: 36 Cov.: 0 AF XY: 0.0170 AC XY: 1225 AN XY: 71978

African (AFR) AF: 0.0329 AC: 1306 AN: 39738

American (AMR) AF: 0.00448 AC: 67 AN: 14968

Ashkenazi Jewish (ASJ) AF: 0.00262 AC: 9 AN: 3430

East Asian (EAS) AF: 0.0137 AC: 68 AN: 4976

South Asian (SAS) AF: 0.00329 AC: 15 AN: 4558

European-Finnish (FIN) AF: 0.0595 AC: 592 AN: 9946

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.00176 AC: 118 AN: 67114

Other (OTH) AF: 0.00984 AC: 20 AN: 2032

Alfa AF: 0.00734 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;