rs10519559

chr5-118608214-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104998.1(LINC02215):n.35-1525C>T variant causes a intron, non coding transcript 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 NR_104998.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02215	NR_104998.1	n.35-1525C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02215	ENST00000503320.1	n.35-1525C>T		intron_variant, non_coding_transcript_variant		4
	ENST00000666304.1	n.450+19515G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0406

Gnomad4 AMR AF: 0.138

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.0175

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.214

Gnomad4 OTH AF: 0.157

Alfa AF: 0.192 Hom.: 2865

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10519559; hg19: chr5-117943909;