rs8081391

Variant names:

• chr17-48694838-G-A
• rs8081391
• ENST00000492522.3:n.52-5774G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000492522.3(LINC02086):​n.52-5774G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,060 control chromosomes in the GnomAD database, including 2,541 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.16 (2541 hom., cov: 31)
• Consequence: LINC02086 ENST00000492522.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593
• Publications: 5 publications found

Genes affected

LINC02086 (HGNC:52936): (long intergenic non-protein coding RNA 2086)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02086	NR_189644.1	n.761-9163G>A		intron_variant	Intron 4 of 5
LINC02086	NR_189645.1	n.4091-5774G>A		intron_variant	Intron 5 of 7
LINC02086	NR_189646.1	n.346-5774G>A		intron_variant	Intron 3 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02086	ENST00000492522.3	n.52-5774G>A		intron_variant	Intron 1 of 3	5
LINC02086	ENST00000575202.3	n.355-9163G>A		intron_variant	Intron 4 of 4	5
LINC02086	ENST00000628006.2	n.574+7128G>A		intron_variant	Intron 5 of 5	5

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24597 AN: 151942 Hom.: 2535 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.283

Gnomad ASJ AF: 0.0864

Gnomad EAS AF: 0.475

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.0836

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.126

Gnomad OTH AF: 0.170

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

GnomAD4 genome AF: 0.162 AC: 24633 AN: 152060 Hom.: 2541 Cov.: 31 AF XY: 0.165 AC XY: 12266 AN XY: 74346

African (AFR) AF: 0.157 AC: 6502 AN: 41486

American (AMR) AF: 0.283 AC: 4322 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0864 AC: 299 AN: 3462

East Asian (EAS) AF: 0.475 AC: 2447 AN: 5148

South Asian (SAS) AF: 0.219 AC: 1055 AN: 4818

European-Finnish (FIN) AF: 0.0836 AC: 886 AN: 10594

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.126 AC: 8569 AN: 67970

Other (OTH) AF: 0.175 AC: 369 AN: 2114

Alfa AF: 0.146 Hom.: 6183

Bravo AF: 0.181

Asia WGS AF: 0.350 AC: 1212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.6
DANN	Benign	0.76
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs8081391; hg19: chr17-46772200;