13-53995230-G-A

Variant names:

• chr13-53995230-G-A
• rs9536579
• ENST00000706980.1:n.465-36800C>T

Variant summary

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

The ENST00000706980.1(LINC00458):​n.465-36800C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.213 in 152,028 control chromosomes in the GnomAD database, including 3,828 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 0.21 (3828 hom., cov: 32)
• Consequence: LINC00458 ENST00000706980.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 4 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.485 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.465-36800C>T		intron_variant	Intron 4 of 10
LINC00458	ENST00000706981.1	n.571-10412C>T		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32397 AN: 151910 Hom.: 3820 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0625

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.216

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.213 AC: 32417 AN: 152028 Hom.: 3828 Cov.: 32 AF XY: 0.213 AC XY: 15838 AN XY: 74300

African (AFR) AF: 0.163 AC: 6767 AN: 41478

American (AMR) AF: 0.186 AC: 2839 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 750 AN: 3466

East Asian (EAS) AF: 0.502 AC: 2581 AN: 5146

South Asian (SAS) AF: 0.265 AC: 1277 AN: 4818

European-Finnish (FIN) AF: 0.216 AC: 2279 AN: 10574

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15310 AN: 67962

Other (OTH) AF: 0.231 AC: 488 AN: 2114

Alfa AF: 0.222 Hom.: 7604

Bravo AF: 0.212

Asia WGS AF: 0.381 AC: 1326 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.82
DANN	Benign	0.44
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs9536579; hg19: chr13-54569365;