12-17576057-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000540399.1(LINC02378):n.763+5762G>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 0.698 in 151,298 control chromosomes in the GnomAD database, including 37,671 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 0.70 (37671 hom., cov: 31)
• Consequence: LINC02378 ENST00000540399.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569

Genes affected

LINC02378 (HGNC:53301): (long intergenic non-protein coding RNA 2378)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.736 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
LINC02378	ENST00000540399.1	n.763+5762G>A		intron_variant, non_coding_transcript_variant		5
	ENST00000669683.1	n.965+71005C>T		intron_variant, non_coding_transcript_variant
LINC02378	ENST00000657845.1	n.451+5762G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.698 AC: 105546 AN: 151178 Hom.: 37659 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.854

Gnomad AMR AF: 0.546

Gnomad ASJ AF: 0.765

Gnomad EAS AF: 0.324

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.744

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.741

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.698 AC: 105589 AN: 151298 Hom.: 37671 Cov.: 31 AF XY: 0.690 AC XY: 50941 AN XY: 73872

Gnomad4 AFR AF: 0.733

Gnomad4 AMR AF: 0.545

Gnomad4 ASJ AF: 0.765

Gnomad4 EAS AF: 0.323

Gnomad4 SAS AF: 0.491

Gnomad4 FIN AF: 0.744

Gnomad4 NFE AF: 0.741

Gnomad4 OTH AF: 0.701

Alfa AF: 0.726 Hom.: 33665

Bravo AF: 0.687

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
Cadd	Benign	14
Dann	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1186300; hg19: chr12-17728991;