15-39251745-T-C

Variant names:

• chr15-39251745-T-C
• rs17691453
• ENST00000561223.1:n.99-314T>C

Variant summary

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

The ENST00000561223.1(LINC02915):​n.99-314T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 151,856 control chromosomes in the GnomAD database, including 16,502 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 0.44 (16502 hom., cov: 32)
• Consequence: LINC02915 ENST00000561223.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.477
• Publications: 5 publications found

Genes affected

LINC02915 (HGNC:33797): (long intergenic non-protein coding RNA 2915)

ENSG00000259345 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.549 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000561223.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02915	NR_144507.1		n.196-203T>C		intron	N/A
	LINC02915	NR_144508.1		n.196-314T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02915	ENST00000561223.1	TSL:1	n.99-314T>C		intron	N/A
	LINC02915	ENST00000625107.2	TSL:1	n.183-203T>C		intron	N/A
	ENSG00000259345	ENST00000558209.1	TSL:3	n.451+108044A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.438 AC: 66459 AN: 151738 Hom.: 16505 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.560

Gnomad EAS AF: 0.207

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.652

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.438 AC: 66468 AN: 151856 Hom.: 16502 Cov.: 32 AF XY: 0.439 AC XY: 32615 AN XY: 74210

African (AFR) AF: 0.223 AC: 9241 AN: 41440

American (AMR) AF: 0.409 AC: 6228 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 1941 AN: 3468

East Asian (EAS) AF: 0.206 AC: 1057 AN: 5120

South Asian (SAS) AF: 0.390 AC: 1872 AN: 4800

European-Finnish (FIN) AF: 0.652 AC: 6887 AN: 10568

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37577 AN: 67910

Other (OTH) AF: 0.442 AC: 932 AN: 2110

Alfa AF: 0.512 Hom.: 85998

Bravo AF: 0.410

Asia WGS AF: 0.297 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.80
PhyloP100		0.48
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs17691453; hg19: chr15-39543946;