14-58897975-C-T

Variant names:

• chr14-58897975-C-T
• rs1427324
• ENST00000553762.2:n.863+3644C>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+3644C>T variant causes a intron 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 ENST00000553762.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.757
• Publications: 4 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=-0.94).
• 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 rank	MANE	Protein	UniProt
LINC01500	NR_110547.1	n.457+3644C>T		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01500	ENST00000553762.2	n.863+3644C>T		intron_variant	Intron 5 of 8	5
LINC01500	ENST00000555378.5	n.457+3644C>T		intron_variant	Intron 2 of 4	3
LINC01500	ENST00000556026.1	n.166+3644C>T		intron_variant	Intron 1 of 3	3

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

African (AFR) AF: 0.0873 AC: 3623 AN: 41504

American (AMR) AF: 0.321 AC: 4899 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3472

East Asian (EAS) AF: 0.602 AC: 3092 AN: 5138

South Asian (SAS) AF: 0.299 AC: 1436 AN: 4810

European-Finnish (FIN) AF: 0.276 AC: 2926 AN: 10590

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.279 AC: 18951 AN: 67962

Other (OTH) AF: 0.278 AC: 586 AN: 2110

Alfa AF: 0.271 Hom.: 7849

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
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1427324; hg19: chr14-59364693;