chr17-53104552-A-G

Variant names:

• chr17-53104552-A-G
• rs1398515
• ENST00000715801.1:n.680-486A>G

Variant summary

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

The ENST00000715801.1(LINC02089):​n.680-486A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,054 control chromosomes in the GnomAD database, including 41,427 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 (41427 hom., cov: 32)
• Consequence: LINC02089 ENST00000715801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 1 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.854 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715801.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02089	ENST00000715801.1		n.680-486A>G		intron	N/A
	LINC02089	ENST00000741187.1		n.120-486A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105140 AN: 151936 Hom.: 41421 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.915

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.742

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.782

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: 0.692 AC: 105156 AN: 152054 Hom.: 41427 Cov.: 32 AF XY: 0.697 AC XY: 51786 AN XY: 74322

African (AFR) AF: 0.277 AC: 11469 AN: 41474

American (AMR) AF: 0.818 AC: 12504 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.853 AC: 2961 AN: 3472

East Asian (EAS) AF: 0.743 AC: 3811 AN: 5132

South Asian (SAS) AF: 0.844 AC: 4065 AN: 4814

European-Finnish (FIN) AF: 0.877 AC: 9296 AN: 10598

Middle Eastern (MID) AF: 0.776 AC: 228 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58418 AN: 67966

Other (OTH) AF: 0.744 AC: 1571 AN: 2112

Alfa AF: 0.774 Hom.: 16344

Bravo AF: 0.668

Asia WGS AF: 0.762 AC: 2649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	9.3
DANN	Benign	0.85
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs1398515; hg19: chr17-51181913;