chr16-86197744-CGTGTGT-C

Variant names:

• chr16-86197744-CGTGTGT-C
• rs58016760
• ENST00000599841.1:n.25-571_25-566delACACAC

Variant summary

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

The ENST00000599841.1(ENSG00000268505):​n.25-571_25-566delACACAC 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 0.0094 (23 hom., cov: 0)
• Consequence: ENSG00000268505 ENST00000599841.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• 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 = 0.00941 (1392/147888) while in subpopulation AFR AF = 0.0328 (1303/39736). AF 95% confidence interval is 0.0313. There are 23 homozygotes in GnomAd4. There are 706 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 23 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01082	NR_103859.1	n.232+1357_232+1362delGTGTGT		intron_variant	Intron 1 of 1
LOC124903743	XR_007065164.1	n.628-571_628-566delACACAC		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000268505	ENST00000599841.1	n.25-571_25-566delACACAC		intron_variant	Intron 1 of 2	4
LINC01082	ENST00000601250.1	n.232+1333_232+1338delGTGTGT		intron_variant	Intron 1 of 1	2
LINC01082	ENST00000669926.3	n.508+1333_508+1338delGTGTGT		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.00938 AC: 1386 AN: 147784 Hom.: 23 Cov.: 0

Gnomad AFR AF: 0.0327

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00368

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00120

Gnomad SAS AF: 0.000438

Gnomad FIN AF: 0.000101

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000253

Gnomad OTH AF: 0.00448

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

GnomAD4 genome AF: 0.00941 AC: 1392 AN: 147888 Hom.: 23 Cov.: 0 AF XY: 0.00981 AC XY: 706 AN XY: 71940

African (AFR) AF: 0.0328 AC: 1303 AN: 39736

American (AMR) AF: 0.00368 AC: 55 AN: 14952

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

East Asian (EAS) AF: 0.00101 AC: 5 AN: 4972

South Asian (SAS) AF: 0.000439 AC: 2 AN: 4558

European-Finnish (FIN) AF: 0.000101 AC: 1 AN: 9936

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.000253 AC: 17 AN: 67080

Other (OTH) AF: 0.00443 AC: 9 AN: 2032

Alfa AF: 0.00 Hom.: 76

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

Other links and lift over

dbSNP: rs58016760; hg19: chr16-86231350;