rs12433225

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000657312.2	n.715+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

African (AFR) AF: 0.225 AC: 9321 AN: 41510

American (AMR) AF: 0.187 AC: 2852 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.269 AC: 933 AN: 3466

East Asian (EAS) AF: 0.158 AC: 815 AN: 5160

South Asian (SAS) AF: 0.146 AC: 702 AN: 4822

European-Finnish (FIN) AF: 0.127 AC: 1349 AN: 10604

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12390 AN: 67974

Other (OTH) AF: 0.212 AC: 447 AN: 2112

Alfa AF: 0.191 Hom.: 1159

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs12433225; hg19: chr14-26526890;