15-52868417-C-T

Variant names:

• chr15-52868417-C-T
• rs2244272
• ENST00000780970.1:n.129-47955C>T

Variant summary

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

The ENST00000780970.1(LINC02490):​n.129-47955C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 152,014 control chromosomes in the GnomAD database, including 14,034 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 0.38 (14034 hom., cov: 32)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.336
• Publications: 8 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.658 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_004837529.2	n.127-47955C>T		intron_variant	Intron 1 of 4
LOC107983981	XR_004837530.2	n.180-47955C>T		intron_variant	Intron 2 of 5
LOC107983981	XR_004837531.2	n.127-47955C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02490	ENST00000780970.1	n.129-47955C>T		intron_variant	Intron 1 of 5
LINC02490	ENST00000780971.1	n.242-47955C>T		intron_variant	Intron 2 of 6
LINC02490	ENST00000780972.1	n.164-47955C>T		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58410 AN: 151896 Hom.: 14009 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.597

Gnomad SAS AF: 0.408

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.385 AC: 58497 AN: 152014 Hom.: 14034 Cov.: 32 AF XY: 0.379 AC XY: 28138 AN XY: 74274

African (AFR) AF: 0.665 AC: 27536 AN: 41432

American (AMR) AF: 0.295 AC: 4506 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1059 AN: 3466

East Asian (EAS) AF: 0.597 AC: 3079 AN: 5160

South Asian (SAS) AF: 0.408 AC: 1961 AN: 4812

European-Finnish (FIN) AF: 0.141 AC: 1488 AN: 10570

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.263 AC: 17890 AN: 67968

Other (OTH) AF: 0.334 AC: 706 AN: 2114

Alfa AF: 0.308 Hom.: 27733

Bravo AF: 0.408

Asia WGS AF: 0.542 AC: 1882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	3.4
DANN	Benign	0.56
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs2244272; hg19: chr15-53160614;