rs390978

Variant names:

• chr12-68394541-A-T
• rs390978
• ENST00000441255.7:n.308-10939T>A

Variant summary

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

The ENST00000539404.1(LINC02384):​n.68+9192T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 152,208 control chromosomes in the GnomAD database, including 3,571 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 0.17 (3571 hom., cov: 32)
• Consequence: LINC02384 ENST00000539404.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 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	ENST00000441255.7	n.308-10939T>A		intron_variant	Intron 3 of 3	4
LINC02384	ENST00000539404.1	n.68+9192T>A		intron_variant	Intron 1 of 1	3
LINC02384	ENST00000546086.1	n.153+47523T>A		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26114 AN: 152090 Hom.: 3568 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.0406

Gnomad AMR AF: 0.0849

Gnomad ASJ AF: 0.0579

Gnomad EAS AF: 0.0241

Gnomad SAS AF: 0.0541

Gnomad FIN AF: 0.0755

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.172 AC: 26147 AN: 152208 Hom.: 3571 Cov.: 32 AF XY: 0.165 AC XY: 12259 AN XY: 74440

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.0848

Gnomad4 ASJ AF: 0.0579

Gnomad4 EAS AF: 0.0243

Gnomad4 SAS AF: 0.0547

Gnomad4 FIN AF: 0.0755

Gnomad4 NFE AF: 0.108

Gnomad4 OTH AF: 0.130

Alfa AF: 0.153 Hom.: 316

Bravo AF: 0.181

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.23
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs390978; hg19: chr12-68788321;