ENST00000642898.1:n.3483T>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-0.9).
• 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

African (AFR) AC: 0 AN: 0

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: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.355 AC: 14724 AN: 41428

American (AMR) AF: 0.234 AC: 3577 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.207 AC: 717 AN: 3472

East Asian (EAS) AF: 0.453 AC: 2337 AN: 5164

South Asian (SAS) AF: 0.225 AC: 1087 AN: 4824

European-Finnish (FIN) AF: 0.342 AC: 3607 AN: 10548

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13631 AN: 67988

Other (OTH) AF: 0.212 AC: 447 AN: 2112

Alfa AF: 0.206 Hom.: 6943

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
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs624797; hg19: chr11-69308575;