chr10-42645787-G-A

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000662977.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01518	ENST00000662977.1		n.744-944C>T		intron	N/A
	LINC01518	ENST00000736721.1		n.522-944C>T		intron	N/A
	ENSG00000285884	ENST00000649715.4		n.*238G>A		downstream_gene	N/A

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 v4.9

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;