rs719715

Variant names:

• chr15-52987094-G-A
• rs719715
• ENST00000780970.1:n.482+11245G>A

Your query was ambiguous. Multiple possible variants found:

• chr15-52987094-G-A
• chr15-52987094-G-C
• chr15-52987094-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.482+11245G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,188 control chromosomes in the GnomAD database, including 49,534 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 0.81 (49534 hom., cov: 34)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.692
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.826 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_001751548.2	n.553+11245G>A		intron_variant	Intron 3 of 3
LOC107983981	XR_004837530.2	n.533+11245G>A		intron_variant	Intron 5 of 5
LOC107983981	XR_004837531.2	n.480+11245G>A		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02490	ENST00000780970.1	n.482+11245G>A		intron_variant	Intron 4 of 5
LINC02490	ENST00000780971.1	n.858+4696G>A		intron_variant	Intron 6 of 6
LINC02490	ENST00000780972.1	n.517+11245G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122711 AN: 152070 Hom.: 49499 Cov.: 34

Gnomad AFR AF: 0.778

Gnomad AMI AF: 0.819

Gnomad AMR AF: 0.838

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.757

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.822

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.807 AC: 122804 AN: 152188 Hom.: 49534 Cov.: 34 AF XY: 0.804 AC XY: 59815 AN XY: 74386

African (AFR) AF: 0.778 AC: 32304 AN: 41528

American (AMR) AF: 0.838 AC: 12813 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2853 AN: 3470

East Asian (EAS) AF: 0.798 AC: 4129 AN: 5176

South Asian (SAS) AF: 0.841 AC: 4057 AN: 4824

European-Finnish (FIN) AF: 0.757 AC: 8010 AN: 10576

Middle Eastern (MID) AF: 0.844 AC: 248 AN: 294

European-Non Finnish (NFE) AF: 0.822 AC: 55923 AN: 68004

Other (OTH) AF: 0.813 AC: 1720 AN: 2116

Alfa AF: 0.819 Hom.: 120724

Bravo AF: 0.810

Asia WGS AF: 0.790 AC: 2743 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs719715; hg19: chr15-53279291;