ENST00000715801.1:n.679+68658A>C

Variant names:

• chr17-52995552-A-C
• rs1512855
• ENST00000715801.1:n.679+68658A>C

Variant summary

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

The ENST00000715801.1(LINC02089):​n.679+68658A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,094 control chromosomes in the GnomAD database, including 12,884 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 0.39 (12884 hom., cov: 32)
• Consequence: LINC02089 ENST00000715801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.28
• Publications: 0 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=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02089	ENST00000715801.1		n.679+68658A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58635 AN: 151974 Hom.: 12884 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.431

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.386

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.396

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

GnomAD4 genome AF: 0.386 AC: 58638 AN: 152094 Hom.: 12884 Cov.: 32 AF XY: 0.388 AC XY: 28814 AN XY: 74322

African (AFR) AF: 0.173 AC: 7173 AN: 41536

American (AMR) AF: 0.431 AC: 6583 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1530 AN: 3466

East Asian (EAS) AF: 0.226 AC: 1168 AN: 5166

South Asian (SAS) AF: 0.387 AC: 1858 AN: 4806

European-Finnish (FIN) AF: 0.540 AC: 5715 AN: 10582

Middle Eastern (MID) AF: 0.452 AC: 132 AN: 292

European-Non Finnish (NFE) AF: 0.489 AC: 33221 AN: 67944

Other (OTH) AF: 0.398 AC: 838 AN: 2108

Alfa AF: 0.447 Hom.: 12346

Bravo AF: 0.371

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	17
DANN	Benign	0.68
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1512855; hg19: chr17-51072912;