17-48680213-G-T

Variant names:

• chr17-48680213-G-T
• rs3096644
• ENST00000575202.3:n.176-3026G>T

Variant summary

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

The NR_189644.1(LINC02086):​n.602-3046G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 152,038 control chromosomes in the GnomAD database, including 16,444 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 0.44 (16444 hom., cov: 32)
• Consequence: LINC02086 NR_189644.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692
• Publications: 12 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_189644.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02086	NR_189644.1		n.602-3046G>T		intron	N/A
	LINC02086	NR_189645.1		n.3886-3046G>T		intron	N/A
	LINC02086	NR_189646.1		n.346-20399G>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02086	ENST00000575202.3	TSL:5	n.176-3026G>T		intron	N/A
	LINC02086	ENST00000628006.2	TSL:5	n.182-3026G>T		intron	N/A
	LINC02086	ENST00000765376.1		n.226-3046G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66316 AN: 151920 Hom.: 16400 Cov.: 32

Gnomad AFR AF: 0.689

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.278

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.437 AC: 66411 AN: 152038 Hom.: 16444 Cov.: 32 AF XY: 0.437 AC XY: 32489 AN XY: 74312

African (AFR) AF: 0.690 AC: 28592 AN: 41458

American (AMR) AF: 0.367 AC: 5607 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1347 AN: 3470

East Asian (EAS) AF: 0.278 AC: 1435 AN: 5166

South Asian (SAS) AF: 0.369 AC: 1779 AN: 4822

European-Finnish (FIN) AF: 0.399 AC: 4218 AN: 10570

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.326 AC: 22162 AN: 67968

Other (OTH) AF: 0.397 AC: 839 AN: 2112

Alfa AF: 0.349 Hom.: 17370

Bravo AF: 0.444

Asia WGS AF: 0.382 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.28
DANN	Benign	0.35
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs3096644; hg19: chr17-46757575;