rs12433225

Variant names:

• chr14-26057684-T-C
• rs12433225
• ENST00000546412.2:n.258+68473A>G

Variant summary

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

The ENST00000546412.2(LINC02306):​n.258+68473A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.19 in 152,134 control chromosomes in the GnomAD database, including 2,825 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 0.19 (2825 hom., cov: 32)
• Consequence: LINC02306 ENST00000546412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

Genes affected

LINC02306 (HGNC:53225): (long intergenic non-protein coding RNA 2306)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 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
LINC02306	ENST00000546412.2	n.258+68473A>G		intron_variant	Intron 2 of 9	3
LINC02306	ENST00000657312.1	n.458+68473A>G		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28918 AN: 152016 Hom.: 2817 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.269

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.190 AC: 28955 AN: 152134 Hom.: 2825 Cov.: 32 AF XY: 0.187 AC XY: 13909 AN XY: 74388

Gnomad4 AFR AF: 0.225

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.269

Gnomad4 EAS AF: 0.158

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.212

Alfa AF: 0.190 Hom.: 757

Bravo AF: 0.197

Asia WGS AF: 0.150 AC: 521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12433225; hg19: chr14-26526890;