15-97064451-C-A

Variant names:

• chr15-97064451-C-A
• rs8023715
• ENST00000740177.1:n.296-26572C>A

Variant summary

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

The ENST00000740177.1(LINC02253):​n.296-26572C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0833 in 152,106 control chromosomes in the GnomAD database, including 569 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 0.083 (569 hom., cov: 33)
• Consequence: LINC02253 ENST00000740177.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.700
• Publications: 10 publications found

Genes affected

LINC02253 (HGNC:53151): (long intergenic non-protein coding RNA 2253)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0987 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
LINC02253	ENST00000740177.1	n.296-26572C>A		intron_variant	Intron 1 of 6
LINC02253	ENST00000740178.1	n.237-26572C>A		intron_variant	Intron 1 of 5
LINC02253	ENST00000740179.1	n.203-26572C>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.0833 AC: 12667 AN: 151988 Hom.: 568 Cov.: 33

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.151

Gnomad AMR AF: 0.0719

Gnomad ASJ AF: 0.0557

Gnomad EAS AF: 0.0389

Gnomad SAS AF: 0.0493

Gnomad FIN AF: 0.0759

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.0825

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

GnomAD4 genome AF: 0.0833 AC: 12676 AN: 152106 Hom.: 569 Cov.: 33 AF XY: 0.0823 AC XY: 6118 AN XY: 74372

African (AFR) AF: 0.101 AC: 4201 AN: 41504

American (AMR) AF: 0.0717 AC: 1095 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0557 AC: 193 AN: 3468

East Asian (EAS) AF: 0.0388 AC: 201 AN: 5178

South Asian (SAS) AF: 0.0495 AC: 239 AN: 4826

European-Finnish (FIN) AF: 0.0759 AC: 803 AN: 10576

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0826 AC: 5617 AN: 67964

Other (OTH) AF: 0.0830 AC: 175 AN: 2108

Alfa AF: 0.0801 Hom.: 1693

Bravo AF: 0.0840

Asia WGS AF: 0.0760 AC: 264 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.69
DANN	Benign	0.45
PhyloP100		-0.70

Splicing

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

Other links and lift over

dbSNP: rs8023715; hg19: chr15-97607681;