rs2086366

chr15-98074012-C-T

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, non coding transcript 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: ENST00000560360.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.815

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000560360.2	n.314-27273G>A		intron_variant, non_coding_transcript_variant		5
LINC02251	ENST00000649950.1	n.393-13126C>T		intron_variant, non_coding_transcript_variant

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;