14-25841023-G-A

Variant names:

• chr14-25841023-G-A
• rs2105274
• ENST00000546412.2:n.259-2493C>T

Variant summary

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

The ENST00000546412.2(LINC02306):​n.259-2493C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 151,710 control chromosomes in the GnomAD database, including 17,844 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 0.44 (17844 hom., cov: 31)
• Consequence: LINC02306 ENST00000546412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.831
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.588 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000546412.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02306	ENST00000546412.2	TSL:3	n.259-2493C>T		intron	N/A
	LINC02306	ENST00000657312.2		n.716-2493C>T		intron	N/A
	LINC02306	ENST00000736906.1		n.63+1601C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67167 AN: 151592 Hom.: 17854 Cov.: 31

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.772

Gnomad AMR AF: 0.514

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.363

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.443 AC: 67155 AN: 151710 Hom.: 17844 Cov.: 31 AF XY: 0.439 AC XY: 32563 AN XY: 74094

African (AFR) AF: 0.142 AC: 5878 AN: 41366

American (AMR) AF: 0.514 AC: 7829 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2143 AN: 3470

East Asian (EAS) AF: 0.363 AC: 1864 AN: 5134

South Asian (SAS) AF: 0.315 AC: 1515 AN: 4802

European-Finnish (FIN) AF: 0.549 AC: 5756 AN: 10494

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40286 AN: 67896

Other (OTH) AF: 0.484 AC: 1016 AN: 2098

Alfa AF: 0.504 Hom.: 2878

Bravo AF: 0.430

Asia WGS AF: 0.308 AC: 1072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.30
DANN	Benign	0.46
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs2105274; hg19: chr14-26310229;