rs486564

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642898.1. 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
	LINC01488	ENST00000642898.1		n.4434T>C		non_coding_transcript_exon	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

African (AFR) AF: 0.250 AC: 1 AN: 4

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 3 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.362 AC: 21 AN: 58

Other (OTH) AF: 0.500 AC: 3 AN: 6

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

African (AFR) AF: 0.407 AC: 16901 AN: 41524

American (AMR) AF: 0.447 AC: 6844 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3466

East Asian (EAS) AF: 0.683 AC: 3524 AN: 5158

South Asian (SAS) AF: 0.401 AC: 1934 AN: 4826

European-Finnish (FIN) AF: 0.516 AC: 5473 AN: 10598

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23122 AN: 67986

Other (OTH) AF: 0.335 AC: 708 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.1
DANN	Benign	0.79
PhyloP100		-0.31

Splicing

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

Other links and lift over

dbSNP: rs486564; hg19: chr11-69309526;