chr13-54006952-A-C

Variant names:

• chr13-54006952-A-C
• rs9536591
• ENST00000706980.1:n.464+46329T>G

Variant summary

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

The ENST00000706980.1(LINC00458):​n.464+46329T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,944 control chromosomes in the GnomAD database, including 15,466 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 0.45 (15466 hom., cov: 32)
• Consequence: LINC00458 ENST00000706980.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 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+46329T>G		intron_variant	Intron 4 of 10
LINC00458	ENST00000706981.1	n.571-22134T>G		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.448 AC: 67983 AN: 151828 Hom.: 15447 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.414

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.490

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.448 AC: 68036 AN: 151944 Hom.: 15466 Cov.: 32 AF XY: 0.446 AC XY: 33075 AN XY: 74240

Gnomad4 AFR AF: 0.429

Gnomad4 AMR AF: 0.391

Gnomad4 ASJ AF: 0.414

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.469

Gnomad4 OTH AF: 0.449

Alfa AF: 0.461 Hom.: 36649

Bravo AF: 0.444

Asia WGS AF: 0.540 AC: 1874 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9536591; hg19: chr13-54581087; COSMIC: COSV53407715;