ENST00000404689.3:n.594-6444G>A

Variant names:

• chr6-92640045-C-T
• rs1841258
• ENST00000404689.3:n.594-6444G>A

Variant summary

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

The ENST00000404689.3(LINC02531):​n.594-6444G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.853 in 152,102 control chromosomes in the GnomAD database, including 56,351 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 0.85 (56351 hom., cov: 32)
• Consequence: LINC02531 ENST00000404689.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 1 publications found

Genes affected

LINC02531 (HGNC:53557): (long intergenic non-protein coding RNA 2531)

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 (NFE) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02531	NR_189297.1	n.506-6447G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02531	ENST00000404689.3	n.594-6444G>A		intron_variant	Intron 2 of 3	5
LINC02531	ENST00000799047.1	n.463-6447G>A		intron_variant	Intron 1 of 2
LINC02531	ENST00000799048.1	n.149-6447G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129742 AN: 151982 Hom.: 56336 Cov.: 32

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.834

Gnomad ASJ AF: 0.929

Gnomad EAS AF: 0.716

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.899

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.868

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.853 AC: 129802 AN: 152102 Hom.: 56351 Cov.: 32 AF XY: 0.851 AC XY: 63277 AN XY: 74346

African (AFR) AF: 0.696 AC: 28888 AN: 41492

American (AMR) AF: 0.835 AC: 12737 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.929 AC: 3225 AN: 3470

East Asian (EAS) AF: 0.716 AC: 3692 AN: 5156

South Asian (SAS) AF: 0.912 AC: 4398 AN: 4822

European-Finnish (FIN) AF: 0.913 AC: 9666 AN: 10588

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.945 AC: 64251 AN: 67990

Other (OTH) AF: 0.865 AC: 1831 AN: 2116

Alfa AF: 0.913 Hom.: 263922

Bravo AF: 0.838

Asia WGS AF: 0.796 AC: 2768 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.73
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1841258; hg19: chr6-93349763;