rs416350

Positions:

• chr12-68385633-G-A
• chr12-68385633-G-C
• chr12-68385633-G-T

Variant summary

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

The ENST00000693550.2(LINC02384):​n.307-51969C>T 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 0.057 in 152,052 control chromosomes in the GnomAD database, including 293 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 0.057 (293 hom., cov: 32)
• Consequence: LINC02384 ENST00000693550.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472

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 (AFR) allele frequency at 95% confidence interval = 0.0737 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.307-51969C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0570 AC: 8662 AN: 151934 Hom.: 293 Cov.: 32

Gnomad AFR AF: 0.0759

Gnomad AMI AF: 0.0385

Gnomad AMR AF: 0.0284

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0235

Gnomad SAS AF: 0.0351

Gnomad FIN AF: 0.0548

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0583

Gnomad OTH AF: 0.0488

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

GnomAD4 genome AF: 0.0570 AC: 8667 AN: 152052 Hom.: 293 Cov.: 32 AF XY: 0.0559 AC XY: 4155 AN XY: 74336

Gnomad4 AFR AF: 0.0759

Gnomad4 AMR AF: 0.0284

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.0237

Gnomad4 SAS AF: 0.0351

Gnomad4 FIN AF: 0.0548

Gnomad4 NFE AF: 0.0583

Gnomad4 OTH AF: 0.0482

Alfa AF: 0.0504 Hom.: 386

Bravo AF: 0.0534

Asia WGS AF: 0.0410 AC: 143 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	1.6
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs416350; hg19: chr12-68779413;