rs2086366

Variant names:

• chr15-98074012-C-T
• rs2086366
• ENST00000560360.2:n.314-27273G>A

Variant summary

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

The ENST00000560360.2(ENSG00000259199):​n.314-27273G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.34 in 151,728 control chromosomes in the GnomAD database, including 9,093 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 0.34 (9093 hom., cov: 32)
• Consequence: ENSG00000259199 ENST00000560360.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815

Genes affected

ENSG00000259199 (HGNC:):

LINC02251 (HGNC:53149): (long intergenic non-protein coding RNA 2251)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.358 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000259199	ENST00000560360.2	n.314-27273G>A		intron_variant	Intron 3 of 4	5
LINC02251	ENST00000649950.1	n.393-13126C>T		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.340 AC: 51511 AN: 151610 Hom.: 9089 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.494

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.373

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.340 AC: 51536 AN: 151728 Hom.: 9093 Cov.: 32 AF XY: 0.346 AC XY: 25632 AN XY: 74102

Gnomad4 AFR AF: 0.286

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.372

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.491

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.319

Alfa AF: 0.347 Hom.: 4460

Bravo AF: 0.326

Asia WGS AF: 0.366 AC: 1275 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.89

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2086366; hg19: chr15-98617241;