ENST00000706980.1:n.464+15086G>A

Variant names:

• chr13-54038195-C-T
• rs4883838
• ENST00000706980.1:n.464+15086G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000706980.1(LINC00458):​n.464+15086G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,002 control chromosomes in the GnomAD database, including 2,655 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 0.18 (2655 hom., cov: 31)
• Consequence: LINC00458 ENST00000706980.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.11

Genes affected

LINC00458 (HGNC:42807): (long intergenic non-protein coding RNA 458)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.254 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00458	ENST00000706980.1	n.464+15086G>A		intron_variant	Intron 4 of 10
LINC00458	ENST00000706981.1	n.571-53377G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27713 AN: 151884 Hom.: 2645 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.124

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.183 AC: 27756 AN: 152002 Hom.: 2655 Cov.: 31 AF XY: 0.184 AC XY: 13695 AN XY: 74276

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.205

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.165

Gnomad4 OTH AF: 0.180

Alfa AF: 0.179 Hom.: 291

Bravo AF: 0.187

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.30
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4883838; hg19: chr13-54612330;