12-68378458-T-C

Variant names:

• chr12-68378458-T-C
• rs4913441
• ENST00000539404.1:n.68+25275A>G

Variant summary

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

The ENST00000539404.1(LINC02384):​n.68+25275A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.9 in 152,238 control chromosomes in the GnomAD database, including 61,800 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 0.90 (61800 hom., cov: 32)
• Consequence: LINC02384 ENST00000539404.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.58
• Publications: 3 publications found

Genes affected

LINC02384 (HGNC:53308): (long intergenic non-protein coding RNA 2384)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000539404.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02384	ENST00000539404.1	TSL:3	n.68+25275A>G		intron	N/A
	LINC02384	ENST00000546086.1	TSL:3	n.154-44794A>G		intron	N/A
	LINC02384	ENST00000686524.3		n.409-44794A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.900 AC: 136940 AN: 152120 Hom.: 61744 Cov.: 32

Gnomad AFR AF: 0.875

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.939

Gnomad EAS AF: 0.976

Gnomad SAS AF: 0.949

Gnomad FIN AF: 0.916

Gnomad MID AF: 0.940

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.919

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

GnomAD4 genome AF: 0.900 AC: 137057 AN: 152238 Hom.: 61800 Cov.: 32 AF XY: 0.903 AC XY: 67248 AN XY: 74436

African (AFR) AF: 0.875 AC: 36345 AN: 41524

American (AMR) AF: 0.949 AC: 14523 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.939 AC: 3260 AN: 3472

East Asian (EAS) AF: 0.976 AC: 5062 AN: 5188

South Asian (SAS) AF: 0.949 AC: 4579 AN: 4826

European-Finnish (FIN) AF: 0.916 AC: 9716 AN: 10606

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60475 AN: 67996

Other (OTH) AF: 0.921 AC: 1946 AN: 2114

Alfa AF: 0.886 Hom.: 18310

Bravo AF: 0.904

Asia WGS AF: 0.953 AC: 3313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.014
DANN	Benign	0.64
PhyloP100		-2.6

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: rs4913441;

hg19: chr12-68772238;