rs9902563

Variant names:

• chr17-43679613-T-C
• rs9902563
• ENST00000593169.2:n.95+178T>C

Variant summary

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

The ENST00000593169.2(LINC02594):​n.95+178T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,248 control chromosomes in the GnomAD database, including 23,045 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 0.54 (23045 hom., cov: 28)
• Consequence: LINC02594 ENST00000593169.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0370
• Publications: 6 publications found

Genes affected

LINC02594 (HGNC:53935): (long intergenic non-protein coding RNA 2594)

ENSG00000305211 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000593169.2. 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
	LINC02594	NR_184089.1		n.189-653T>C		intron	N/A
	LINC02594	NR_184090.1		n.374+178T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02594	ENST00000593169.2	TSL:4	n.95+178T>C		intron	N/A
	ENSG00000305211	ENST00000809649.1		n.322+1392A>G		intron	N/A
	ENSG00000305211	ENST00000809650.1		n.200-2548A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81050 AN: 151132 Hom.: 23019 Cov.: 28

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.430

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.391

Gnomad EAS AF: 0.511

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.564

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.536 AC: 81116 AN: 151248 Hom.: 23045 Cov.: 28 AF XY: 0.538 AC XY: 39720 AN XY: 73812

African (AFR) AF: 0.738 AC: 30441 AN: 41260

American (AMR) AF: 0.481 AC: 7326 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.391 AC: 1353 AN: 3464

East Asian (EAS) AF: 0.510 AC: 2585 AN: 5066

South Asian (SAS) AF: 0.493 AC: 2347 AN: 4760

European-Finnish (FIN) AF: 0.564 AC: 5910 AN: 10474

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.437 AC: 29586 AN: 67712

Other (OTH) AF: 0.510 AC: 1065 AN: 2090

Alfa AF: 0.459 Hom.: 9802

Bravo AF: 0.543

Asia WGS AF: 0.470 AC: 1633 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.80
PhyloP100		0.037

Splicing

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

Other links and lift over

dbSNP: rs9902563; hg19: chr17-41756981;