15-52952920-A-T

Variant names:

• chr15-52952920-A-T
• rs727614
• ENST00000780970.1:n.197-18483A>T

Variant summary

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

The ENST00000780970.1(LINC02490):​n.197-18483A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,172 control chromosomes in the GnomAD database, including 2,543 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 0.18 (2543 hom., cov: 32)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.615
• Publications: 3 publications found

Genes affected

LINC02490 (HGNC:53471): (long intergenic non-protein coding RNA 2490)

LOC107983981 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780970.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02490	ENST00000780970.1		n.197-18483A>T		intron	N/A
	LINC02490	ENST00000780971.1		n.310-18483A>T		intron	N/A
	LINC02490	ENST00000780972.1		n.232-18483A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26644 AN: 152052 Hom.: 2545 Cov.: 32

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.0301

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.175 AC: 26636 AN: 152172 Hom.: 2543 Cov.: 32 AF XY: 0.171 AC XY: 12707 AN XY: 74388

African (AFR) AF: 0.153 AC: 6338 AN: 41498

American (AMR) AF: 0.167 AC: 2553 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3468

East Asian (EAS) AF: 0.0303 AC: 157 AN: 5176

South Asian (SAS) AF: 0.125 AC: 603 AN: 4818

European-Finnish (FIN) AF: 0.123 AC: 1304 AN: 10612

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14477 AN: 67996

Other (OTH) AF: 0.201 AC: 424 AN: 2108

Alfa AF: 0.0735 Hom.: 106

Bravo AF: 0.175

Asia WGS AF: 0.0710 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.53
PhyloP100		0.61

Splicing

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

Other links and lift over

dbSNP: rs727614; hg19: chr15-53245117;