rs158389

Positions:

• chr10-42645787-G-A

Variant summary

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

The ENST00000662977.1(LINC01518):​n.744-944C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 151,804 control chromosomes in the GnomAD database, including 7,693 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 0.29 (7693 hom., cov: 30)
• Consequence: LINC01518 ENST00000662977.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891

Genes affected

LINC01518 (HGNC:51216): (long intergenic non-protein coding RNA 1518)

ACMG classification

Verdict is Benign. Variant got -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 = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01518	ENST00000662977.1	n.744-944C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44607 AN: 151686 Hom.: 7680 Cov.: 30

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.381

Gnomad OTH AF: 0.314

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

GnomAD4 genome AF: 0.294 AC: 44620 AN: 151804 Hom.: 7693 Cov.: 30 AF XY: 0.295 AC XY: 21846 AN XY: 74162

Gnomad4 AFR AF: 0.108

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.450

Gnomad4 SAS AF: 0.390

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.381

Gnomad4 OTH AF: 0.316

Alfa AF: 0.366 Hom.: 5358

Bravo AF: 0.282

Asia WGS AF: 0.403 AC: 1397 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	4.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs158389; hg19: chr10-43141235;