ENST00000539404.1:n.69-12688G>C

Variant names:

• chr12-68346352-C-G
• rs7971639
• ENST00000539404.1:n.69-12688G>C

Variant summary

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

The ENST00000539404.1(LINC02384):​n.69-12688G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.682 in 152,104 control chromosomes in the GnomAD database, including 35,689 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 0.68 (35689 hom., cov: 32)
• Consequence: LINC02384 ENST00000539404.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.720

Genes affected

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

ENSG00000256273 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.58).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.691 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.69-12688G>C		intron_variant	Intron 1 of 1	3
ENSG00000256273	ENST00000544089.1	n.240+1449C>G		intron_variant	Intron 1 of 1	2
LINC02384	ENST00000546086.1	n.154-12688G>C		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.682 AC: 103720 AN: 151986 Hom.: 35679 Cov.: 32

Gnomad AFR AF: 0.681

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.702

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.605

Gnomad FIN AF: 0.734

Gnomad MID AF: 0.706

Gnomad NFE AF: 0.690

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.682 AC: 103778 AN: 152104 Hom.: 35689 Cov.: 32 AF XY: 0.681 AC XY: 50659 AN XY: 74354

Gnomad4 AFR AF: 0.681

Gnomad4 AMR AF: 0.702

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.605

Gnomad4 FIN AF: 0.734

Gnomad4 NFE AF: 0.690

Gnomad4 OTH AF: 0.688

Alfa AF: 0.676 Hom.: 3596

Bravo AF: 0.681

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	7.4
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7971639; hg19: chr12-68740132;