ENST00000539404.1:n.69-8659G>A

Variant names:

• chr12-68342323-C-T
• rs10878810
• ENST00000539404.1:n.69-8659G>A

Variant summary

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

The ENST00000539404.1(LINC02384):​n.69-8659G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,152 control chromosomes in the GnomAD database, including 4,766 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 0.24 (4766 hom., cov: 32)
• Consequence: LINC02384 ENST00000539404.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476
• Publications: 6 publications found

Genes affected

LINC02384 (HGNC:53308): (long intergenic non-protein coding RNA 2384)

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 (SAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000539404.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02384	ENST00000539404.1	TSL:3	n.69-8659G>A		intron	N/A
	LINC02384	ENST00000546086.1	TSL:3	n.154-8659G>A		intron	N/A
	LINC02384	ENST00000653144.2		n.81+6178G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36345 AN: 152034 Hom.: 4770 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.285

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

GnomAD4 genome AF: 0.239 AC: 36358 AN: 152152 Hom.: 4766 Cov.: 32 AF XY: 0.234 AC XY: 17443 AN XY: 74390

African (AFR) AF: 0.136 AC: 5643 AN: 41532

American (AMR) AF: 0.259 AC: 3967 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.397 AC: 1380 AN: 3472

East Asian (EAS) AF: 0.178 AC: 921 AN: 5178

South Asian (SAS) AF: 0.333 AC: 1605 AN: 4816

European-Finnish (FIN) AF: 0.172 AC: 1824 AN: 10580

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20102 AN: 67964

Other (OTH) AF: 0.288 AC: 608 AN: 2114

Alfa AF: 0.287 Hom.: 5613

Bravo AF: 0.240

Asia WGS AF: 0.268 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.50
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs10878810; hg19: chr12-68736103;