14-58705860-T-C

Variant names:

• chr14-58705860-T-C
• rs7153749
• ENST00000648996.1:n.536+12454T>C

Variant summary

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

The ENST00000648996.1(LINC01500):​n.536+12454T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,024 control chromosomes in the GnomAD database, including 15,100 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 0.44 (15100 hom., cov: 32)
• Consequence: LINC01500 ENST00000648996.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.136
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01500	ENST00000648996.1	n.536+12454T>C		intron_variant	Intron 3 of 13

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66685 AN: 151908 Hom.: 15079 Cov.: 32

Gnomad AFR AF: 0.341

Gnomad AMI AF: 0.528

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.432

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

GnomAD4 genome AF: 0.439 AC: 66752 AN: 152024 Hom.: 15100 Cov.: 32 AF XY: 0.445 AC XY: 33052 AN XY: 74314

African (AFR) AF: 0.341 AC: 14130 AN: 41450

American (AMR) AF: 0.482 AC: 7362 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1193 AN: 3466

East Asian (EAS) AF: 0.515 AC: 2660 AN: 5166

South Asian (SAS) AF: 0.317 AC: 1529 AN: 4824

European-Finnish (FIN) AF: 0.610 AC: 6441 AN: 10562

Middle Eastern (MID) AF: 0.428 AC: 125 AN: 292

European-Non Finnish (NFE) AF: 0.470 AC: 31910 AN: 67958

Other (OTH) AF: 0.437 AC: 924 AN: 2114

Alfa AF: 0.451 Hom.: 33411

Bravo AF: 0.431

Asia WGS AF: 0.423 AC: 1471 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.65
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs7153749; hg19: chr14-59172578;