17-53025561-A-C

Variant names:

• chr17-53025561-A-C
• rs792774
• ENST00000715801.1:n.680-79477A>C

Variant summary

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

The ENST00000715801.1(LINC02089):​n.680-79477A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,664 control chromosomes in the GnomAD database, including 13,322 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 0.40 (13322 hom., cov: 30)
• Consequence: LINC02089 ENST00000715801.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.483 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02089	ENST00000715801.1		n.680-79477A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60538 AN: 151542 Hom.: 13319 Cov.: 30

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.441

Gnomad EAS AF: 0.226

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.487

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.399 AC: 60557 AN: 151664 Hom.: 13322 Cov.: 30 AF XY: 0.401 AC XY: 29725 AN XY: 74058

African (AFR) AF: 0.216 AC: 8931 AN: 41374

American (AMR) AF: 0.466 AC: 7089 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.441 AC: 1525 AN: 3460

East Asian (EAS) AF: 0.225 AC: 1156 AN: 5136

South Asian (SAS) AF: 0.376 AC: 1807 AN: 4804

European-Finnish (FIN) AF: 0.532 AC: 5581 AN: 10484

Middle Eastern (MID) AF: 0.449 AC: 131 AN: 292

European-Non Finnish (NFE) AF: 0.487 AC: 33060 AN: 67884

Other (OTH) AF: 0.408 AC: 858 AN: 2104

Alfa AF: 0.445 Hom.: 7377

Bravo AF: 0.386

Asia WGS AF: 0.303 AC: 1055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.37
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs792774; hg19: chr17-51102921;