chr17-53103164-C-T

Variant names:

• chr17-53103164-C-T
• rs2137476
• ENST00000715801.1:n.680-1874C>T

Variant summary

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

The ENST00000715801.1(LINC02089):​n.680-1874C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.7 in 151,996 control chromosomes in the GnomAD database, including 41,819 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 0.70 (41819 hom., cov: 31)
• Consequence: LINC02089 ENST00000715801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.73
• 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=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.853 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.680-1874C>T		intron	N/A
	LINC02089	ENST00000741187.1		n.120-1874C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.701 AC: 106422 AN: 151878 Hom.: 41809 Cov.: 31

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.916

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.853

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.877

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.859

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.700 AC: 106447 AN: 151996 Hom.: 41819 Cov.: 31 AF XY: 0.705 AC XY: 52376 AN XY: 74272

African (AFR) AF: 0.307 AC: 12737 AN: 41452

American (AMR) AF: 0.821 AC: 12538 AN: 15264

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

East Asian (EAS) AF: 0.744 AC: 3808 AN: 5120

South Asian (SAS) AF: 0.844 AC: 4059 AN: 4808

European-Finnish (FIN) AF: 0.877 AC: 9301 AN: 10604

Middle Eastern (MID) AF: 0.781 AC: 228 AN: 292

European-Non Finnish (NFE) AF: 0.859 AC: 58399 AN: 67962

Other (OTH) AF: 0.749 AC: 1581 AN: 2110

Alfa AF: 0.789 Hom.: 19305

Bravo AF: 0.678

Asia WGS AF: 0.766 AC: 2660 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.10
DANN	Benign	0.47
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2137476; hg19: chr17-51180525;