rs4883887

chr13-54248030-A-G

Variant summary

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

The ENST00000706980.1(LINC00458):n.119+21212T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 151,960 control chromosomes in the GnomAD database, including 833 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 0.091 (833 hom., cov: 31)
• Consequence: LINC00458 ENST00000706980.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.415

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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00458	ENST00000706980.1	n.119+21212T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13812 AN: 151842 Hom.: 831 Cov.: 31

Gnomad AFR AF: 0.0509

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.0165

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.0793

Gnomad MID AF: 0.0924

Gnomad NFE AF: 0.0949

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.0910 AC: 13823 AN: 151960 Hom.: 833 Cov.: 31 AF XY: 0.0939 AC XY: 6976 AN XY: 74256

Gnomad4 AFR AF: 0.0511

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.0801

Gnomad4 EAS AF: 0.0166

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.0793

Gnomad4 NFE AF: 0.0950

Gnomad4 OTH AF: 0.100

Alfa AF: 0.114 Hom.: 245

Bravo AF: 0.0980

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.1
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4883887; hg19: chr13-54822165;