12-68378458-T-C

Variant names:

• chr12-68378458-T-C
• rs4913441
• ENST00000539404.1:n.68+25275A>G

Variant summary

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

The ENST00000539404.1(LINC02384):​n.68+25275A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 152,238 control chromosomes in the GnomAD database, including 61,800 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 0.90 (61800 hom., cov: 32)
• Consequence: LINC02384 ENST00000539404.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02384	ENST00000539404.1	n.68+25275A>G		intron_variant	Intron 1 of 1	3
LINC02384	ENST00000546086.1	n.154-44794A>G		intron_variant	Intron 1 of 1	3
LINC02384	ENST00000686524.2	n.390-44794A>G		intron_variant	Intron 2 of 2
LINC02384	ENST00000693550.2	n.307-44794A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136940 AN: 152120 Hom.: 61744 Cov.: 32

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.900 AC: 137057 AN: 152238 Hom.: 61800 Cov.: 32 AF XY: 0.903 AC XY: 67248 AN XY: 74436

Gnomad4 AFR AF: 0.875

Gnomad4 AMR AF: 0.949

Gnomad4 ASJ AF: 0.939

Gnomad4 EAS AF: 0.976

Gnomad4 SAS AF: 0.949

Gnomad4 FIN AF: 0.916

Gnomad4 NFE AF: 0.889

Gnomad4 OTH AF: 0.921

Alfa AF: 0.883 Hom.: 9670

Bravo AF: 0.904

Asia WGS AF: 0.953 AC: 3313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.014
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4913441; hg19: chr12-68772238;