rs390978

Positions:

• chr12-68394541-A-T

Variant summary

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

The ENST00000693550.2(LINC02384):​n.306+56826T>A 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 0.172 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 ENST00000693550.2 intron, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02384	ENST00000693550.2	n.306+56826T>A		intron_variant, non_coding_transcript_variant

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;