11-69493807-T-G

Variant names:

• chr11-69493807-T-G
• rs624797
• ENST00000642898.1:n.3483T>G

Variant summary

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

The ENST00000642898.1(LINC01488):​n.3483T>G 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 0.265 in 152,034 control chromosomes in the GnomAD database, including 5,810 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 0.26 (5810 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LINC01488 ENST00000642898.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 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.3483T>G		non_coding_transcript_exon_variant	Exon 7 of 7

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40254 AN: 151914 Hom.: 5807 Cov.: 33

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.207

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.201

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.265 AC: 40286 AN: 152032 Hom.: 5810 Cov.: 33 AF XY: 0.272 AC XY: 20198 AN XY: 74314

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.234

Gnomad4 ASJ AF: 0.207

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.225

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.212

Alfa AF: 0.199 Hom.: 4728

Bravo AF: 0.261

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs624797; hg19: chr11-69308575;