rs4883887

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.191 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+21212T>C		intron	N/A
	LINC00458	ENST00000706981.1		n.199+20109T>C		intron	N/A
	LINC00458	ENST00000706986.1		n.73+20109T>C		intron	N/A

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

African (AFR) AF: 0.0511 AC: 2118 AN: 41482

American (AMR) AF: 0.184 AC: 2799 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.0801 AC: 278 AN: 3472

East Asian (EAS) AF: 0.0166 AC: 85 AN: 5130

South Asian (SAS) AF: 0.202 AC: 972 AN: 4820

European-Finnish (FIN) AF: 0.0793 AC: 840 AN: 10596

Middle Eastern (MID) AF: 0.0925 AC: 27 AN: 292

European-Non Finnish (NFE) AF: 0.0950 AC: 6450 AN: 67928

Other (OTH) AF: 0.100 AC: 212 AN: 2112

Alfa AF: 0.112 Hom.: 245

Bravo AF: 0.0980

Asia WGS AF: 0.111 AC: 385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.1
DANN	Benign	0.67
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs4883887; hg19: chr13-54822165;