chr15-53141694-G-T

Variant names:

• chr15-53141694-G-T
• rs565439
• ENST00000780970.1:n.633+12305G>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+12305G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.987 in 152,218 control chromosomes in the GnomAD database, including 74,108 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 0.99 (74108 hom., cov: 30)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.629
• 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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.994 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_001751548.2	n.554-51934G>T		intron_variant	Intron 3 of 3
LOC107983981	XR_004837530.2	n.534-51934G>T		intron_variant	Intron 5 of 5
LOC107983981	XR_004837531.2	n.481-79732G>T		intron_variant	Intron 4 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02490	ENST00000780970.1	n.633+12305G>T		intron_variant	Intron 5 of 5
LINC02490	ENST00000780976.1	n.228+12305G>T		intron_variant	Intron 2 of 3
LINC02490	ENST00000780978.1	n.228+12305G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.987 AC: 150058 AN: 152100 Hom.: 74058 Cov.: 30

Gnomad AFR AF: 0.953

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.996

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 1.00

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.997

Gnomad NFE AF: 1.00

Gnomad OTH AF: 0.992

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

GnomAD4 genome AF: 0.987 AC: 150167 AN: 152218 Hom.: 74108 Cov.: 30 AF XY: 0.987 AC XY: 73450 AN XY: 74424

African (AFR) AF: 0.953 AC: 39559 AN: 41516

American (AMR) AF: 0.996 AC: 15235 AN: 15302

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5166 AN: 5166

South Asian (SAS) AF: 1.00 AC: 4817 AN: 4818

European-Finnish (FIN) AF: 1.00 AC: 10612 AN: 10612

Middle Eastern (MID) AF: 0.997 AC: 293 AN: 294

European-Non Finnish (NFE) AF: 1.00 AC: 68005 AN: 68014

Other (OTH) AF: 0.992 AC: 2096 AN: 2112

Alfa AF: 0.992 Hom.: 9492

Bravo AF: 0.985

Asia WGS AF: 0.997 AC: 3467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.96
DANN	Benign	0.47
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs565439; hg19: chr15-53433891;