ENST00000715800.1:n.683-1161G>T

Variant names:

• chr17-52984354-G-T
• rs1512867
• ENST00000715800.1:n.683-1161G>T

Variant summary

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

The ENST00000715800.1(LINC02089):​n.683-1161G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,962 control chromosomes in the GnomAD database, including 14,029 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 0.41 (14029 hom., cov: 32)
• Consequence: LINC02089 ENST00000715800.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.640
• 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=-0.89).
• 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.683-1161G>T		intron_variant	Intron 4 of 7
LINC02089	ENST00000715801.1	n.679+57460G>T		intron_variant	Intron 4 of 4
LINC02089	ENST00000753155.1	n.680-1161G>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63008 AN: 151842 Hom.: 14025 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.423

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

GnomAD4 genome AF: 0.415 AC: 63048 AN: 151962 Hom.: 14029 Cov.: 32 AF XY: 0.417 AC XY: 30980 AN XY: 74274

African (AFR) AF: 0.260 AC: 10789 AN: 41440

American (AMR) AF: 0.477 AC: 7283 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1619 AN: 3470

East Asian (EAS) AF: 0.225 AC: 1160 AN: 5150

South Asian (SAS) AF: 0.386 AC: 1861 AN: 4824

European-Finnish (FIN) AF: 0.534 AC: 5631 AN: 10546

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

European-Non Finnish (NFE) AF: 0.489 AC: 33259 AN: 67948

Other (OTH) AF: 0.423 AC: 892 AN: 2108

Alfa AF: 0.451 Hom.: 2368

Bravo AF: 0.403

Asia WGS AF: 0.325 AC: 1130 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.38
DANN	Benign	0.69
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs1512867; hg19: chr17-51061714;