12-17576057-C-T

Variant names:

• chr12-17576057-C-T
• rs1186300
• ENST00000540399.1:n.763+5762G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000540399.1(LINC02378):​n.763+5762G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.569
• Publications: 4 publications found

Genes affected

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

ENSG00000256389 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02378	ENST00000540399.1	n.763+5762G>A		intron_variant	Intron 6 of 7	5
LINC02378	ENST00000657845.1	n.451+5762G>A		intron_variant	Intron 5 of 6
ENSG00000256389	ENST00000669683.1	n.965+71005C>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.733 AC: 30232 AN: 41264

American (AMR) AF: 0.545 AC: 8280 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.765 AC: 2645 AN: 3458

East Asian (EAS) AF: 0.323 AC: 1648 AN: 5106

South Asian (SAS) AF: 0.491 AC: 2369 AN: 4824

European-Finnish (FIN) AF: 0.744 AC: 7801 AN: 10482

Middle Eastern (MID) AF: 0.777 AC: 227 AN: 292

European-Non Finnish (NFE) AF: 0.741 AC: 50134 AN: 67660

Other (OTH) AF: 0.701 AC: 1478 AN: 2108

Alfa AF: 0.721 Hom.: 57071

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
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs1186300; hg19: chr12-17728991;