rs7178476

Variant names:

• chr15-52870887-A-G
• rs7178476
• ENST00000780970.1:n.129-45485A>G

Variant summary

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

The ENST00000780970.1(LINC02490):​n.129-45485A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,114 control chromosomes in the GnomAD database, including 9,362 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 0.33 (9362 hom., cov: 32)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.300
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.494 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.129-45485A>G		intron	N/A
	LINC02490	ENST00000780971.1		n.242-45485A>G		intron	N/A
	LINC02490	ENST00000780972.1		n.164-45485A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50134 AN: 151996 Hom.: 9346 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.301

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.139

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.262

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.330 AC: 50203 AN: 152114 Hom.: 9362 Cov.: 32 AF XY: 0.325 AC XY: 24186 AN XY: 74344

African (AFR) AF: 0.499 AC: 20726 AN: 41502

American (AMR) AF: 0.277 AC: 4239 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.301 AC: 1044 AN: 3464

East Asian (EAS) AF: 0.414 AC: 2132 AN: 5144

South Asian (SAS) AF: 0.392 AC: 1891 AN: 4820

European-Finnish (FIN) AF: 0.139 AC: 1469 AN: 10604

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.262 AC: 17800 AN: 67980

Other (OTH) AF: 0.299 AC: 632 AN: 2112

Alfa AF: 0.290 Hom.: 20831

Bravo AF: 0.346

Asia WGS AF: 0.459 AC: 1593 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.83
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7178476; hg19: chr15-53163084;