ENST00000513875.5:n.389-1873T>C

Variant names:

• chr4-129810129-T-C
• rs4864201
• ENST00000513875.5:n.389-1873T>C

Variant summary

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

The ENST00000513875.5(LINC02465):​n.389-1873T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.485 in 151,926 control chromosomes in the GnomAD database, including 20,615 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 0.48 (20615 hom., cov: 32)
• Consequence: LINC02465 ENST00000513875.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184
• Publications: 21 publications found

Genes affected

LINC02465 (HGNC:53403): (long intergenic non-protein coding RNA 2465)

LINC02466 (HGNC:53405): (long intergenic non-protein coding RNA 2466)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.646 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000513875.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02465	NR_151713.1		n.429-1873T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02465	ENST00000513875.5	TSL:5	n.389-1873T>C		intron	N/A
	LINC02465	ENST00000652794.1		n.183-1873T>C		intron	N/A
	LINC02465	ENST00000653703.1		n.446-1873T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.485 AC: 73634 AN: 151808 Hom.: 20625 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.466

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.591

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.485 AC: 73635 AN: 151926 Hom.: 20615 Cov.: 32 AF XY: 0.481 AC XY: 35706 AN XY: 74226

African (AFR) AF: 0.219 AC: 9068 AN: 41476

American (AMR) AF: 0.466 AC: 7086 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1748 AN: 3464

East Asian (EAS) AF: 0.271 AC: 1395 AN: 5152

South Asian (SAS) AF: 0.461 AC: 2225 AN: 4824

European-Finnish (FIN) AF: 0.591 AC: 6236 AN: 10554

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.651 AC: 44203 AN: 67930

Other (OTH) AF: 0.486 AC: 1027 AN: 2112

Alfa AF: 0.579 Hom.: 57953

Bravo AF: 0.461

Asia WGS AF: 0.318 AC: 1104 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.78
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs4864201; hg19: chr4-130731284;