13-54180396-T-C

Variant names:

• chr13-54180396-T-C
• rs632059
• ENST00000706980.1:n.120-52967A>G

Variant summary

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

The ENST00000706980.1(LINC00458):​n.120-52967A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.965 in 152,208 control chromosomes in the GnomAD database, including 70,906 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 0.96 (70906 hom., cov: 31)
• Consequence: LINC00458 ENST00000706980.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.376

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.968 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.120-52967A>G		intron_variant	Intron 1 of 10
LINC00458	ENST00000706981.1	n.200-52967A>G		intron_variant	Intron 2 of 5
LINC00458	ENST00000706986.1	n.110+2988A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.965 AC: 146771 AN: 152090 Hom.: 70857 Cov.: 31

Gnomad AFR AF: 0.952

Gnomad AMI AF: 0.988

Gnomad AMR AF: 0.972

Gnomad ASJ AF: 0.974

Gnomad EAS AF: 0.893

Gnomad SAS AF: 0.991

Gnomad FIN AF: 0.975

Gnomad MID AF: 1.00

Gnomad NFE AF: 0.972

Gnomad OTH AF: 0.967

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

GnomAD4 genome AF: 0.965 AC: 146878 AN: 152208 Hom.: 70906 Cov.: 31 AF XY: 0.965 AC XY: 71819 AN XY: 74408

Gnomad4 AFR AF: 0.952

Gnomad4 AMR AF: 0.973

Gnomad4 ASJ AF: 0.974

Gnomad4 EAS AF: 0.893

Gnomad4 SAS AF: 0.991

Gnomad4 FIN AF: 0.975

Gnomad4 NFE AF: 0.972

Gnomad4 OTH AF: 0.965

Alfa AF: 0.971 Hom.: 8341

Bravo AF: 0.963

Asia WGS AF: 0.954 AC: 3315 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.97
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs632059; hg19: chr13-54754531;