rs2086366

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

ENSG00000259199 (HGNC:):

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

LINC01582 (HGNC:51416): (long intergenic non-protein coding RNA 1582)

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 (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
LINC01582	ENST00000717123.1	n.513-27273G>A		intron_variant	Intron 1 of 3
ENSG00000259199	ENST00000717124.1	n.292-27273G>A		intron_variant	Intron 3 of 8

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

African (AFR) AF: 0.286 AC: 11836 AN: 41390

American (AMR) AF: 0.329 AC: 5025 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1085 AN: 3458

East Asian (EAS) AF: 0.372 AC: 1921 AN: 5160

South Asian (SAS) AF: 0.351 AC: 1688 AN: 4812

European-Finnish (FIN) AF: 0.491 AC: 5166 AN: 10518

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23601 AN: 67822

Other (OTH) AF: 0.319 AC: 673 AN: 2110

Alfa AF: 0.348 Hom.: 4930

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
PhyloP100		-0.81

Splicing

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

Other links and lift over

dbSNP: rs2086366; hg19: chr15-98617241;