chr13-54006952-A-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000706980.1. 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
	LINC00458	ENST00000706980.1		n.464+46329T>G		intron	N/A
	LINC00458	ENST00000706981.1		n.571-22134T>G		intron	N/A

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

African (AFR) AF: 0.429 AC: 17793 AN: 41462

American (AMR) AF: 0.391 AC: 5965 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.414 AC: 1437 AN: 3472

East Asian (EAS) AF: 0.601 AC: 3095 AN: 5150

South Asian (SAS) AF: 0.492 AC: 2362 AN: 4800

European-Finnish (FIN) AF: 0.382 AC: 4037 AN: 10562

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.469 AC: 31866 AN: 67950

Other (OTH) AF: 0.449 AC: 943 AN: 2102

Alfa AF: 0.461 Hom.: 73568

Bravo AF: 0.444

Asia WGS AF: 0.540 AC: 1874 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.52
PhyloP100		-0.48

Splicing

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

Other links and lift over

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