14-58897975-C-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+3644C>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 0.241 in 152,064 control chromosomes in the GnomAD database, including 5,405 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 0.24 (5405 hom., cov: 32)
• Consequence: LINC01500 NR_110547.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01500	NR_110547.1	n.457+3644C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01500	ENST00000648996.1	n.1412+3644C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36614 AN: 151946 Hom.: 5406 Cov.: 32

Gnomad AFR AF: 0.0872

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.601

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.279

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.241 AC: 36620 AN: 152064 Hom.: 5405 Cov.: 32 AF XY: 0.246 AC XY: 18305 AN XY: 74342

Gnomad4 AFR AF: 0.0873

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.299

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.279

Gnomad4 OTH AF: 0.278

Alfa AF: 0.274 Hom.: 5166

Bravo AF: 0.242

Asia WGS AF: 0.432 AC: 1504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.85
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1427324; hg19: chr14-59364693;