17-53065559-A-T

Variant names:

• chr17-53065559-A-T
• rs1858465
• ENST00000715801.1:n.680-39479A>T

Variant summary

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

The ENST00000715801.1(LINC02089):​n.680-39479A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.691 in 151,992 control chromosomes in the GnomAD database, including 41,378 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 0.69 (41378 hom., cov: 32)
• Consequence: LINC02089 ENST00000715801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490
• Publications: 9 publications found

Genes affected

LINC02089 (HGNC:52940): (long intergenic non-protein coding RNA 2089)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02089	ENST00000715801.1	n.680-39479A>T		intron_variant	Intron 4 of 4
LINC02089	ENST00000741187.1	n.119+1221A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105026 AN: 151874 Hom.: 41371 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.741

Gnomad SAS AF: 0.844

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.783

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.691 AC: 105043 AN: 151992 Hom.: 41378 Cov.: 32 AF XY: 0.696 AC XY: 51736 AN XY: 74300

African (AFR) AF: 0.276 AC: 11444 AN: 41474

American (AMR) AF: 0.818 AC: 12485 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2957 AN: 3468

East Asian (EAS) AF: 0.741 AC: 3820 AN: 5154

South Asian (SAS) AF: 0.843 AC: 4057 AN: 4812

European-Finnish (FIN) AF: 0.877 AC: 9255 AN: 10558

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.859 AC: 58393 AN: 67952

Other (OTH) AF: 0.744 AC: 1570 AN: 2110

Alfa AF: 0.763 Hom.: 5978

Bravo AF: 0.668

Asia WGS AF: 0.762 AC: 2623 AN: 3446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.9
DANN	Benign	0.72
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs1858465; hg19: chr17-51142920;