rs486564

Variant names:

• chr11-69494758-T-C
• rs486564
• ENST00000642898.1:n.4434T>C

Variant summary

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

The ENST00000642898.1(LINC01488):​n.4434T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.394 in 152,250 control chromosomes in the GnomAD database, including 12,208 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 0.39 (12201 hom., cov: 34)
  • Exomes 𝑓: 0.38 (7 hom.)
• Consequence: LINC01488 ENST00000642898.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.309

Genes affected

LINC01488 (HGNC:51144): (long intergenic non-protein coding RNA 1488)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.664 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
LINC01488	ENST00000642898.1	n.4434T>C		non_coding_transcript_exon_variant	Exon 7 of 7

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59891 AN: 152058 Hom.: 12186 Cov.: 34

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.317

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.684

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.330

GnomAD4 exome AF: 0.378 AC: 28 AN: 74 Hom.: 7 Cov.: 0 AF XY: 0.315 AC XY: 17 AN XY: 54

Gnomad4 AFR exome AF: 0.250

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.362

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.394 AC: 59951 AN: 152176 Hom.: 12201 Cov.: 34 AF XY: 0.406 AC XY: 30224 AN XY: 74396

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.683

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.516

Gnomad4 NFE AF: 0.340

Gnomad4 OTH AF: 0.335

Alfa AF: 0.379 Hom.: 1407

Bravo AF: 0.389

Asia WGS AF: 0.553 AC: 1917 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs486564; hg19: chr11-69309526;