14-58899597-G-T

Variant names:

• chr14-58899597-G-T
• rs405460
• ENST00000553762.2:n.863+5266G>T

Variant summary

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

The ENST00000553762.2(LINC01500):​n.863+5266G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,976 control chromosomes in the GnomAD database, including 10,615 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 0.35 (10615 hom., cov: 33)
• Consequence: LINC01500 ENST00000553762.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 9 publications found

Genes affected

LINC01500 (HGNC:51166): (long intergenic non-protein coding RNA 1500)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553762.2. 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
	LINC01500	NR_110547.1		n.457+5266G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01500	ENST00000553762.2	TSL:5	n.863+5266G>T		intron	N/A
	LINC01500	ENST00000555378.5	TSL:3	n.457+5266G>T		intron	N/A
	LINC01500	ENST00000556026.1	TSL:3	n.166+5266G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53669 AN: 151858 Hom.: 10620 Cov.: 33

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.695

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.353 AC: 53691 AN: 151976 Hom.: 10615 Cov.: 33 AF XY: 0.356 AC XY: 26420 AN XY: 74304

African (AFR) AF: 0.170 AC: 7031 AN: 41440

American (AMR) AF: 0.401 AC: 6123 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1148 AN: 3468

East Asian (EAS) AF: 0.695 AC: 3595 AN: 5172

South Asian (SAS) AF: 0.401 AC: 1928 AN: 4810

European-Finnish (FIN) AF: 0.365 AC: 3856 AN: 10552

Middle Eastern (MID) AF: 0.339 AC: 99 AN: 292

European-Non Finnish (NFE) AF: 0.423 AC: 28730 AN: 67944

Other (OTH) AF: 0.377 AC: 796 AN: 2110

Alfa AF: 0.395 Hom.: 39419

Bravo AF: 0.350

Asia WGS AF: 0.524 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.40
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs405460; hg19: chr14-59366315;