rs10519559

Variant names:

• chr5-118608214-C-T
• rs10519559
• ENST00000503320.1:n.35-1525C>T

Variant summary

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

The ENST00000503320.1(LINC02215):​n.35-1525C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,130 control chromosomes in the GnomAD database, including 1,998 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 0.14 (1998 hom., cov: 32)
• Consequence: LINC02215 ENST00000503320.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25
• Publications: 6 publications found

Genes affected

LINC02215 (HGNC:53082): (long intergenic non-protein coding RNA 2215)

ENSG00000286745 (HGNC:):

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 = 0.212 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02215	NR_104998.1	n.35-1525C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02215	ENST00000503320.1	n.35-1525C>T		intron_variant	Intron 1 of 4	4
ENSG00000286745	ENST00000666304.1	n.450+19515G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21553 AN: 152012 Hom.: 1997 Cov.: 32

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0175

Gnomad SAS AF: 0.105

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.214

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.142 AC: 21548 AN: 152130 Hom.: 1998 Cov.: 32 AF XY: 0.138 AC XY: 10243 AN XY: 74384

African (AFR) AF: 0.0406 AC: 1684 AN: 41510

American (AMR) AF: 0.138 AC: 2105 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 440 AN: 3468

East Asian (EAS) AF: 0.0175 AC: 91 AN: 5186

South Asian (SAS) AF: 0.106 AC: 510 AN: 4808

European-Finnish (FIN) AF: 0.160 AC: 1687 AN: 10574

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.214 AC: 14580 AN: 67980

Other (OTH) AF: 0.157 AC: 332 AN: 2112

Alfa AF: 0.185 Hom.: 3394

Bravo AF: 0.135

Asia WGS AF: 0.0440 AC: 155 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	1.0
DANN	Benign	0.58
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs10519559; hg19: chr5-117943909;