rs4883887

Variant names:

• chr13-54248030-A-G
• rs4883887
• ENST00000706980.1:n.119+21212T>C

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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00458	ENST00000706980.1	n.119+21212T>C		intron_variant	Intron 1 of 10
LINC00458	ENST00000706981.1	n.199+20109T>C		intron_variant	Intron 2 of 5
LINC00458	ENST00000706986.1	n.73+20109T>C		intron_variant	Intron 1 of 2

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;