ENST00000543778.2:n.404+407A>G

Variant names:

• chr12-20125332-T-C
• rs7964046
• ENST00000543778.2:n.404+407A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000543778.2(LINC02468):​n.404+407A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 151,940 control chromosomes in the GnomAD database, including 22,419 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 0.53 (22419 hom., cov: 32)
• Consequence: LINC02468 ENST00000543778.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 3 publications found

Genes affected

LINC02468 (HGNC:53406): (long intergenic non-protein coding RNA 2468)

ENSG00000255910 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.704 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000543778.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02468	NR_146523.1		n.183+407A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02468	ENST00000543778.2	TSL:5	n.404+407A>G		intron	N/A
	LINC02468	ENST00000655042.1		n.468+395A>G		intron	N/A
	LINC02468	ENST00000655208.1		n.416+407A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.528 AC: 80184 AN: 151822 Hom.: 22397 Cov.: 32

Gnomad AFR AF: 0.711

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.517

Gnomad EAS AF: 0.351

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.510

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.538

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

GnomAD4 genome AF: 0.528 AC: 80255 AN: 151940 Hom.: 22419 Cov.: 32 AF XY: 0.529 AC XY: 39309 AN XY: 74260

African (AFR) AF: 0.711 AC: 29477 AN: 41454

American (AMR) AF: 0.536 AC: 8179 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.517 AC: 1794 AN: 3468

East Asian (EAS) AF: 0.350 AC: 1803 AN: 5150

South Asian (SAS) AF: 0.448 AC: 2159 AN: 4824

European-Finnish (FIN) AF: 0.510 AC: 5381 AN: 10554

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29876 AN: 67928

Other (OTH) AF: 0.536 AC: 1130 AN: 2108

Alfa AF: 0.466 Hom.: 71660

Bravo AF: 0.539

Asia WGS AF: 0.409 AC: 1421 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.5
DANN	Benign	0.32
PhyloP100		-0.53

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7964046;

hg19: chr12-20278266;