ENST00000780970.1:n.129-42160G>A

Variant names:

• chr15-52874212-G-A
• rs2120445
• ENST00000780970.1:n.129-42160G>A

Variant summary

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

The ENST00000780970.1(LINC02490):​n.129-42160G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.83 in 152,176 control chromosomes in the GnomAD database, including 52,732 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 0.83 (52732 hom., cov: 31)
• Consequence: LINC02490 ENST00000780970.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0590
• 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.875 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107983981	XR_004837529.2	n.127-42160G>A		intron_variant	Intron 1 of 4
LOC107983981	XR_004837530.2	n.180-42160G>A		intron_variant	Intron 2 of 5
LOC107983981	XR_004837531.2	n.127-42160G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02490	ENST00000780970.1	n.129-42160G>A		intron_variant	Intron 1 of 5
LINC02490	ENST00000780971.1	n.242-42160G>A		intron_variant	Intron 2 of 6
LINC02490	ENST00000780972.1	n.164-42160G>A		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.830 AC: 126233 AN: 152058 Hom.: 52689 Cov.: 31

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.886

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.866

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.811

Gnomad FIN AF: 0.866

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.815

Gnomad OTH AF: 0.838

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

GnomAD4 genome AF: 0.830 AC: 126317 AN: 152176 Hom.: 52732 Cov.: 31 AF XY: 0.830 AC XY: 61719 AN XY: 74380

African (AFR) AF: 0.883 AC: 36653 AN: 41514

American (AMR) AF: 0.704 AC: 10761 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.866 AC: 3004 AN: 3470

East Asian (EAS) AF: 0.878 AC: 4535 AN: 5166

South Asian (SAS) AF: 0.811 AC: 3904 AN: 4814

European-Finnish (FIN) AF: 0.866 AC: 9177 AN: 10600

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.815 AC: 55436 AN: 68002

Other (OTH) AF: 0.840 AC: 1774 AN: 2112

Alfa AF: 0.819 Hom.: 71726

Bravo AF: 0.818

Asia WGS AF: 0.838 AC: 2913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		0.059

Splicing

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

Other links and lift over

dbSNP: rs2120445; hg19: chr15-53166409;