rs158389

Variant names:

• chr10-42645787-G-A
• rs158389
• ENST00000662977.1:n.744-944C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

Genes affected

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

ENSG00000285884 (HGNC:):

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 = 0.435 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105378268	XR_007062124.1	n.*245G>A		downstream_gene_variant
LOC105378268	XR_007062125.1	n.*245G>A		downstream_gene_variant
LOC105378268	XR_945898.3	n.*245G>A		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01518	ENST00000662977.1	n.744-944C>T		intron_variant	Intron 7 of 7
LINC01518	ENST00000736721.1	n.522-944C>T		intron_variant	Intron 5 of 5
ENSG00000285884	ENST00000649715.4	n.*238G>A		downstream_gene_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

African (AFR) AF: 0.108 AC: 4455 AN: 41420

American (AMR) AF: 0.298 AC: 4543 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1190 AN: 3466

East Asian (EAS) AF: 0.450 AC: 2308 AN: 5128

South Asian (SAS) AF: 0.390 AC: 1872 AN: 4802

European-Finnish (FIN) AF: 0.313 AC: 3294 AN: 10514

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.381 AC: 25889 AN: 67916

Other (OTH) AF: 0.316 AC: 662 AN: 2096

Alfa AF: 0.359 Hom.: 7454

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
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs158389; hg19: chr10-43141235;