rs719714

Variant names:

• chr15-52987181-A-G
• rs719714
• ENST00000780970.1:n.482+11332A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-52987181-A-G
• chr15-52987181-A-T

Variant summary

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

The ENST00000780970.1(LINC02490):​n.482+11332A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0767 in 152,296 control chromosomes in the GnomAD database, including 670 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 0.077 (670 hom., cov: 33)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0310
• Publications: 11 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.267 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_001751548.2	n.553+11332A>G		intron_variant	Intron 3 of 3
LOC107983981	XR_004837530.2	n.533+11332A>G		intron_variant	Intron 5 of 5
LOC107983981	XR_004837531.2	n.480+11332A>G		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02490	ENST00000780970.1	n.482+11332A>G		intron_variant	Intron 4 of 5
LINC02490	ENST00000780971.1	n.858+4783A>G		intron_variant	Intron 6 of 6
LINC02490	ENST00000780972.1	n.517+11332A>G		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.0767 AC: 11677 AN: 152178 Hom.: 670 Cov.: 33

Gnomad AFR AF: 0.0659

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.280

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0584

Gnomad OTH AF: 0.0860

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

GnomAD4 genome AF: 0.0767 AC: 11675 AN: 152296 Hom.: 670 Cov.: 33 AF XY: 0.0812 AC XY: 6048 AN XY: 74490

African (AFR) AF: 0.0660 AC: 2743 AN: 41572

American (AMR) AF: 0.101 AC: 1550 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.104 AC: 359 AN: 3468

East Asian (EAS) AF: 0.278 AC: 1443 AN: 5182

South Asian (SAS) AF: 0.226 AC: 1090 AN: 4826

European-Finnish (FIN) AF: 0.0249 AC: 264 AN: 10622

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.0585 AC: 3977 AN: 68020

Other (OTH) AF: 0.0899 AC: 190 AN: 2114

Alfa AF: 0.0684 Hom.: 2150

Bravo AF: 0.0789

Asia WGS AF: 0.244 AC: 846 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.7
DANN	Benign	0.52
PhyloP100		-0.031

Splicing

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

Other links and lift over

dbSNP: rs719714; hg19: chr15-53279378;