chr15-53203733-T-C

Variant names:

• chr15-53203733-T-C
• rs518127
• ENST00000780988.1:n.310-5126T>C

Variant summary

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

The ENST00000780988.1(LINC02490):​n.310-5126T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,972 control chromosomes in the GnomAD database, including 8,130 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 0.32 (8130 hom., cov: 32)
• Consequence: LINC02490 ENST00000780988.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_004837531.2	n.481-17693T>C		intron_variant	Intron 4 of 4
LOC107983981	XR_932257.3	n.696+9890T>C		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02490	ENST00000780988.1	n.310-5126T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.323 AC: 49025 AN: 151854 Hom.: 8118 Cov.: 32

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.389

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.500

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.323 AC: 49072 AN: 151972 Hom.: 8130 Cov.: 32 AF XY: 0.332 AC XY: 24643 AN XY: 74292

African (AFR) AF: 0.300 AC: 12457 AN: 41468

American (AMR) AF: 0.389 AC: 5939 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.317 AC: 1101 AN: 3470

East Asian (EAS) AF: 0.500 AC: 2561 AN: 5120

South Asian (SAS) AF: 0.380 AC: 1829 AN: 4808

European-Finnish (FIN) AF: 0.392 AC: 4144 AN: 10574

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20122 AN: 67954

Other (OTH) AF: 0.315 AC: 664 AN: 2108

Alfa AF: 0.301 Hom.: 21069

Bravo AF: 0.324

Asia WGS AF: 0.434 AC: 1507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs518127; hg19: chr15-53495930;