ENST00000780970.1:n.128+36242T>C

Variant names:

• chr15-52840866-T-C
• rs1317318
• ENST00000780970.1:n.128+36242T>C

Variant summary

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

The ENST00000780970.1(LINC02490):​n.128+36242T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,234 control chromosomes in the GnomAD database, including 911 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 0.11 (911 hom., cov: 32)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.708
• 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=-0.59).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.149 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_004837529.2	n.126+36242T>C		intron_variant	Intron 1 of 4
LOC107983981	XR_004837530.2	n.179+36242T>C		intron_variant	Intron 2 of 5
LOC107983981	XR_004837531.2	n.126+36242T>C		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02490	ENST00000780970.1	n.128+36242T>C		intron_variant	Intron 1 of 5
LINC02490	ENST00000780971.1	n.241+36242T>C		intron_variant	Intron 2 of 6
LINC02490	ENST00000780972.1	n.163+36242T>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16138 AN: 152116 Hom.: 909 Cov.: 32

Gnomad AFR AF: 0.152

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.0547

Gnomad ASJ AF: 0.0977

Gnomad EAS AF: 0.0314

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.0437

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.106 AC: 16171 AN: 152234 Hom.: 911 Cov.: 32 AF XY: 0.104 AC XY: 7707 AN XY: 74426

African (AFR) AF: 0.152 AC: 6302 AN: 41528

American (AMR) AF: 0.0546 AC: 836 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0977 AC: 339 AN: 3470

East Asian (EAS) AF: 0.0319 AC: 165 AN: 5178

South Asian (SAS) AF: 0.151 AC: 729 AN: 4818

European-Finnish (FIN) AF: 0.0437 AC: 464 AN: 10610

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 6980 AN: 68010

Other (OTH) AF: 0.0999 AC: 211 AN: 2112

Alfa AF: 0.108 Hom.: 164

Bravo AF: 0.106

Asia WGS AF: 0.0960 AC: 337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	14
DANN	Benign	0.90
PhyloP100		0.71

Splicing

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

Other links and lift over

dbSNP: rs1317318; hg19: chr15-53133063;