ENST00000780970.1:n.197-18723C>T

Variant names:

• chr15-52952680-C-T
• rs716188
• ENST00000780970.1:n.197-18723C>T

Variant summary

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

The ENST00000780970.1(LINC02490):​n.197-18723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0511 in 152,282 control chromosomes in the GnomAD database, including 390 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 0.051 (390 hom., cov: 33)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000780970.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02490	ENST00000780970.1		n.197-18723C>T		intron	N/A
	LINC02490	ENST00000780971.1		n.310-18723C>T		intron	N/A
	LINC02490	ENST00000780972.1		n.232-18723C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0511 AC: 7773 AN: 152164 Hom.: 390 Cov.: 33

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0773

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.0137

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.0101

Gnomad OTH AF: 0.0502

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

GnomAD4 genome AF: 0.0511 AC: 7788 AN: 152282 Hom.: 390 Cov.: 33 AF XY: 0.0515 AC XY: 3832 AN XY: 74466

African (AFR) AF: 0.110 AC: 4572 AN: 41536

American (AMR) AF: 0.0779 AC: 1191 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3470

East Asian (EAS) AF: 0.185 AC: 960 AN: 5188

South Asian (SAS) AF: 0.0162 AC: 78 AN: 4826

European-Finnish (FIN) AF: 0.0137 AC: 145 AN: 10618

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0101 AC: 688 AN: 68026

Other (OTH) AF: 0.0516 AC: 109 AN: 2114

Alfa AF: 0.0406 Hom.: 41

Bravo AF: 0.0626

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.73
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs716188; hg19: chr15-53244877;