chr17-52984063-T-C

Variant names:

• chr17-52984063-T-C
• rs1512868
• ENST00000715800.1:n.683-1452T>C

Variant summary

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

The ENST00000715800.1(LINC02089):​n.683-1452T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 151,964 control chromosomes in the GnomAD database, including 14,393 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 0.42 (14393 hom., cov: 31)
• Consequence: LINC02089 ENST00000715800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.64
• Publications: 4 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=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 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	ENST00000715800.1	n.683-1452T>C		intron_variant	Intron 4 of 7
LINC02089	ENST00000715801.1	n.679+57169T>C		intron_variant	Intron 4 of 4
LINC02089	ENST00000753155.1	n.680-1452T>C		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64252 AN: 151846 Hom.: 14386 Cov.: 31

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.461

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.422

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

GnomAD4 genome AF: 0.423 AC: 64302 AN: 151964 Hom.: 14393 Cov.: 31 AF XY: 0.425 AC XY: 31539 AN XY: 74260

African (AFR) AF: 0.296 AC: 12292 AN: 41472

American (AMR) AF: 0.480 AC: 7324 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.466 AC: 1616 AN: 3468

East Asian (EAS) AF: 0.175 AC: 903 AN: 5150

South Asian (SAS) AF: 0.386 AC: 1863 AN: 4828

European-Finnish (FIN) AF: 0.534 AC: 5628 AN: 10546

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33230 AN: 67922

Other (OTH) AF: 0.422 AC: 892 AN: 2112

Alfa AF: 0.460 Hom.: 61959

Bravo AF: 0.413

Asia WGS AF: 0.310 AC: 1081 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.0
DANN	Benign	0.72
PhyloP100		2.6

Splicing

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

Other links and lift over

dbSNP: rs1512868; hg19: chr17-51061423;