rs10878810

chr12-68342323-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000693550.2(LINC02384):n.307-8659G>A variant causes a intron, non coding transcript 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 ENST00000693550.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02384	ENST00000693550.2	n.307-8659G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.136

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.333

Gnomad4 FIN AF: 0.172

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.288

Alfa AF: 0.289 Hom.: 4762

Bravo AF: 0.240

Asia WGS AF: 0.268 AC: 933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.2
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10878810; hg19: chr12-68736103;