rs2120445

Variant names:

• chr15-52874212-G-A
• rs2120445
• ENST00000780970.1:n.129-42160G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-52874212-G-A
• chr15-52874212-G-T

Variant summary

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

The ENST00000780970.1(LINC02490):​n.129-42160G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,176 control chromosomes in the GnomAD database, including 52,732 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 0.83 (52732 hom., cov: 31)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• Publications: 4 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 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.129-42160G>A		intron	N/A
	LINC02490	ENST00000780971.1		n.242-42160G>A		intron	N/A
	LINC02490	ENST00000780972.1		n.164-42160G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126233 AN: 152058 Hom.: 52689 Cov.: 31

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.830 AC: 126317 AN: 152176 Hom.: 52732 Cov.: 31 AF XY: 0.830 AC XY: 61719 AN XY: 74380

African (AFR) AF: 0.883 AC: 36653 AN: 41514

American (AMR) AF: 0.704 AC: 10761 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3004 AN: 3470

East Asian (EAS) AF: 0.878 AC: 4535 AN: 5166

South Asian (SAS) AF: 0.811 AC: 3904 AN: 4814

European-Finnish (FIN) AF: 0.866 AC: 9177 AN: 10600

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55436 AN: 68002

Other (OTH) AF: 0.840 AC: 1774 AN: 2112

Alfa AF: 0.819 Hom.: 71726

Bravo AF: 0.818

Asia WGS AF: 0.838 AC: 2913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		0.059

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: rs2120445;

hg19: chr15-53166409;