rs1762642

Variant names:

• chr10-42667691-T-C
• rs1762642
• ENST00000662977.1:n.689+4871A>G

Variant summary

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

The ENST00000662977.1(LINC01518):​n.689+4871A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0322 in 151,976 control chromosomes in the GnomAD database, including 213 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 0.032 (213 hom., cov: 32)
• Consequence: LINC01518 ENST00000662977.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550
• Publications: 1 publications found

Genes affected

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

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 = 0.127 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01518	ENST00000662977.1		n.689+4871A>G		intron	N/A
	LINC01518	ENST00000736721.1		n.467+6717A>G		intron	N/A
	LINC01518	ENST00000736722.1		n.533-5975A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0323 AC: 4900 AN: 151858 Hom.: 215 Cov.: 32

Gnomad AFR AF: 0.0882

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0115

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.0607

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000456

Gnomad OTH AF: 0.0258

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

GnomAD4 genome AF: 0.0322 AC: 4895 AN: 151976 Hom.: 213 Cov.: 32 AF XY: 0.0334 AC XY: 2483 AN XY: 74242

African (AFR) AF: 0.0879 AC: 3644 AN: 41436

American (AMR) AF: 0.0115 AC: 175 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3464

East Asian (EAS) AF: 0.135 AC: 698 AN: 5156

South Asian (SAS) AF: 0.0604 AC: 289 AN: 4788

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10566

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.000456 AC: 31 AN: 67980

Other (OTH) AF: 0.0255 AC: 54 AN: 2114

Alfa AF: 0.0223 Hom.: 13

Bravo AF: 0.0349

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.79
DANN	Benign	0.41
PhyloP100		0.055

Splicing

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

Other links and lift over

dbSNP: rs1762642; hg19: chr10-43163139;