15-98063084-G-A

Variant names:

• chr15-98063084-G-A
• rs1993976
• ENST00000560360.2:n.314-16345C>T

Variant summary

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

The ENST00000560360.2(ENSG00000259199):​n.314-16345C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,846 control chromosomes in the GnomAD database, including 15,295 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 0.45 (15295 hom., cov: 32)
• Consequence: ENSG00000259199 ENST00000560360.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.225
• Publications: 9 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.471 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.314-16345C>T		intron_variant	Intron 3 of 4	5
LINC02251	ENST00000649950.1	n.393-24054G>A		intron_variant	Intron 3 of 3
LINC01582	ENST00000717123.1	n.513-16345C>T		intron_variant	Intron 1 of 3
ENSG00000259199	ENST00000717124.1	n.292-16345C>T		intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67803 AN: 151728 Hom.: 15282 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.412

Gnomad FIN AF: 0.513

Gnomad MID AF: 0.356

Gnomad NFE AF: 0.434

Gnomad OTH AF: 0.431

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

GnomAD4 genome AF: 0.447 AC: 67853 AN: 151846 Hom.: 15295 Cov.: 32 AF XY: 0.448 AC XY: 33258 AN XY: 74234

African (AFR) AF: 0.476 AC: 19715 AN: 41382

American (AMR) AF: 0.421 AC: 6429 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.411 AC: 1422 AN: 3464

East Asian (EAS) AF: 0.377 AC: 1927 AN: 5112

South Asian (SAS) AF: 0.411 AC: 1979 AN: 4812

European-Finnish (FIN) AF: 0.513 AC: 5407 AN: 10550

Middle Eastern (MID) AF: 0.359 AC: 104 AN: 290

European-Non Finnish (NFE) AF: 0.434 AC: 29515 AN: 67952

Other (OTH) AF: 0.430 AC: 906 AN: 2106

Alfa AF: 0.441 Hom.: 13817

Bravo AF: 0.443

Asia WGS AF: 0.412 AC: 1438 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.78
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs1993976; hg19: chr15-98606313;