13-54260889-T-C

Variant names:

• chr13-54260889-T-C
• rs2818224
• ENST00000706980.1:n.119+8353A>G

Variant summary

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

The ENST00000706980.1(LINC00458):​n.119+8353A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0807 in 151,350 control chromosomes in the GnomAD database, including 665 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 0.081 (665 hom., cov: 32)
• Consequence: LINC00458 ENST00000706980.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 0 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.173 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.119+8353A>G		intron	N/A
	LINC00458	ENST00000706981.1		n.199+7250A>G		intron	N/A
	LINC00458	ENST00000706986.1		n.73+7250A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0807 AC: 12203 AN: 151232 Hom.: 660 Cov.: 32

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.00974

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.0592

Gnomad MID AF: 0.135

Gnomad NFE AF: 0.0832

Gnomad OTH AF: 0.0958

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

GnomAD4 genome AF: 0.0807 AC: 12221 AN: 151350 Hom.: 665 Cov.: 32 AF XY: 0.0818 AC XY: 6049 AN XY: 73970

African (AFR) AF: 0.0471 AC: 1947 AN: 41348

American (AMR) AF: 0.179 AC: 2715 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3470

East Asian (EAS) AF: 0.00977 AC: 50 AN: 5120

South Asian (SAS) AF: 0.117 AC: 563 AN: 4810

European-Finnish (FIN) AF: 0.0592 AC: 617 AN: 10424

Middle Eastern (MID) AF: 0.134 AC: 39 AN: 290

European-Non Finnish (NFE) AF: 0.0833 AC: 5638 AN: 67694

Other (OTH) AF: 0.0948 AC: 199 AN: 2100

Alfa AF: 0.0826 Hom.: 139

Bravo AF: 0.0914

Asia WGS AF: 0.0680 AC: 238 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.099
DANN	Benign	0.64
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs2818224; hg19: chr13-54835024;