rs382518

chr12-68386307-T-C

Variant summary

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

The ENST00000693550.2(LINC02384):n.307-52643A>G 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 0.115 in 152,180 control chromosomes in the GnomAD database, including 1,193 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 0.11 (1193 hom., cov: 32)
• Consequence: LINC02384 ENST00000693550.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.02

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=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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.307-52643A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17461 AN: 152062 Hom.: 1195 Cov.: 32

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0407

Gnomad AMR AF: 0.0591

Gnomad ASJ AF: 0.0519

Gnomad EAS AF: 0.0239

Gnomad SAS AF: 0.0532

Gnomad FIN AF: 0.0831

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.0884

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

GnomAD4 genome AF: 0.115 AC: 17469 AN: 152180 Hom.: 1193 Cov.: 32 AF XY: 0.111 AC XY: 8250 AN XY: 74410

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0590

Gnomad4 ASJ AF: 0.0519

Gnomad4 EAS AF: 0.0241

Gnomad4 SAS AF: 0.0538

Gnomad4 FIN AF: 0.0831

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.0870

Alfa AF: 0.101 Hom.: 853

Bravo AF: 0.113

Asia WGS AF: 0.0530 AC: 184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	16
Dann	Benign	0.93

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs382518; hg19: chr12-68780087;