chr15-39251745-T-C

Position:

• chr15-39251745-T-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LINC02915 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02915	NR_144507.1	n.196-203T>C		intron_variant
LINC02915	NR_144508.1	n.196-314T>C		intron_variant
LOC105370777	XR_007064588.1	n.517+168799A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02915	ENST00000561223.1	n.99-314T>C		intron_variant		1
LINC02915	ENST00000625107.1	n.181-203T>C		intron_variant		1
ENSG00000259345	ENST00000558209.1	n.451+108044A>G		intron_variant		3

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

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.560

Gnomad4 EAS AF: 0.206

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.652

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.442

Alfa AF: 0.525 Hom.: 42044

Bravo AF: 0.410

Asia WGS AF: 0.297 AC: 1030 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.6
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17691453; hg19: chr15-39543946;