ENST00000642898.1:n.3805C>T

Variant names:

• chr11-69494129-C-T
• rs623110
• ENST00000642898.1:n.3805C>T

Variant summary

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

The ENST00000642898.1(LINC01488):​n.3805C>T 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 152,040 control chromosomes in the GnomAD database, including 12,181 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 (12180 hom., cov: 33)
  • Exomes 𝑓: 0.46 (1 hom.)
• Consequence: LINC01488 ENST00000642898.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.740
• Publications: 3 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=-0.91).
• 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.3805C>T		non_coding_transcript_exon_variant	Exon 7 of 7

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59813 AN: 151894 Hom.: 12165 Cov.: 33

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.329

GnomAD4 exome AF: 0.464 AC: 13 AN: 28 Hom.: 1 Cov.: 0 AF XY: 0.500 AC XY: 11 AN XY: 22

African (AFR) AC: 0 AN: 0

American (AMR) AF: 1.00 AC: 2 AN: 2

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: 2 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.409 AC: 9 AN: 22

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.394 AC: 59873 AN: 152012 Hom.: 12180 Cov.: 33 AF XY: 0.406 AC XY: 30176 AN XY: 74300

African (AFR) AF: 0.407 AC: 16877 AN: 41452

American (AMR) AF: 0.447 AC: 6843 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3470

East Asian (EAS) AF: 0.683 AC: 3504 AN: 5134

South Asian (SAS) AF: 0.401 AC: 1933 AN: 4822

European-Finnish (FIN) AF: 0.516 AC: 5456 AN: 10574

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

European-Non Finnish (NFE) AF: 0.340 AC: 23106 AN: 67950

Other (OTH) AF: 0.334 AC: 706 AN: 2112

Alfa AF: 0.352 Hom.: 6235

Bravo AF: 0.389

Asia WGS AF: 0.549 AC: 1904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.14
DANN	Benign	0.69
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs623110; hg19: chr11-69308897;