rs12595250

Variant names:

• chr15-53132765-C-T
• rs12595250
• ENST00000780970.1:n.633+3376C>T

Variant summary

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

The ENST00000780970.1(LINC02490):​n.633+3376C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0684 in 152,254 control chromosomes in the GnomAD database, including 541 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 0.068 (541 hom., cov: 33)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.489
• Publications: 0 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 (EAS) allele frequency at 95% confidence interval = 0.272 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02490	ENST00000780970.1		n.633+3376C>T		intron	N/A
	LINC02490	ENST00000780976.1		n.228+3376C>T		intron	N/A
	LINC02490	ENST00000780978.1		n.228+3376C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0684 AC: 10405 AN: 152136 Hom.: 542 Cov.: 33

Gnomad AFR AF: 0.0368

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0932

Gnomad ASJ AF: 0.0326

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0630

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0642

Gnomad OTH AF: 0.0766

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

GnomAD4 genome AF: 0.0684 AC: 10416 AN: 152254 Hom.: 541 Cov.: 33 AF XY: 0.0719 AC XY: 5351 AN XY: 74450

African (AFR) AF: 0.0368 AC: 1531 AN: 41564

American (AMR) AF: 0.0938 AC: 1434 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0326 AC: 113 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1472 AN: 5174

South Asian (SAS) AF: 0.130 AC: 627 AN: 4822

European-Finnish (FIN) AF: 0.0630 AC: 669 AN: 10612

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0642 AC: 4367 AN: 68010

Other (OTH) AF: 0.0773 AC: 163 AN: 2110

Alfa AF: 0.0645 Hom.: 195

Bravo AF: 0.0678

Asia WGS AF: 0.192 AC: 666 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	1.4
DANN	Benign	0.28
PhyloP100		-0.49

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12595250;

hg19: chr15-53424962;