chr14-25681304-C-T

Variant names:

• chr14-25681304-C-T
• rs12893752
• ENST00000546412.2:n.538-16329G>A

Variant summary

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

The ENST00000546412.2(LINC02306):​n.538-16329G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.348 in 152,174 control chromosomes in the GnomAD database, including 11,291 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 0.35 (11291 hom., cov: 33)
• Consequence: LINC02306 ENST00000546412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.509
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.461 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.538-16329G>A		intron_variant	Intron 5 of 9	3
LINC02306	ENST00000736904.1	n.280-16329G>A		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.348 AC: 52984 AN: 152056 Hom.: 11292 Cov.: 33

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.545

Gnomad AMR AF: 0.391

Gnomad ASJ AF: 0.503

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.348 AC: 52979 AN: 152174 Hom.: 11291 Cov.: 33 AF XY: 0.349 AC XY: 25978 AN XY: 74388

African (AFR) AF: 0.109 AC: 4511 AN: 41512

American (AMR) AF: 0.391 AC: 5981 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.503 AC: 1746 AN: 3472

East Asian (EAS) AF: 0.182 AC: 942 AN: 5174

South Asian (SAS) AF: 0.312 AC: 1508 AN: 4828

European-Finnish (FIN) AF: 0.492 AC: 5207 AN: 10586

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31612 AN: 67994

Other (OTH) AF: 0.398 AC: 842 AN: 2116

Alfa AF: 0.432 Hom.: 62948

Bravo AF: 0.332

Asia WGS AF: 0.242 AC: 845 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.2
DANN	Benign	0.77
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs12893752; hg19: chr14-26150510;