14-58899597-G-T

Variant summary

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

The NR_110547.1(LINC01500):n.457+5266G>T 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 0.353 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 NR_110547.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01500	NR_110547.1	n.457+5266G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01500	ENST00000648996.1	n.1412+5266G>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.695

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.377

Alfa AF: 0.406 Hom.: 26649

Bravo AF: 0.350

Asia WGS AF: 0.524 AC: 1824 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.3
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs405460; hg19: chr14-59366315;