ENST00000546412.2:n.538-2430G>T

Variant names:

• chr14-25667405-C-A
• rs1475010
• ENST00000546412.2:n.538-2430G>T

Variant summary

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

The ENST00000546412.2(LINC02306):​n.538-2430G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 151,798 control chromosomes in the GnomAD database, including 19,402 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 0.47 (19402 hom., cov: 31)
• Consequence: LINC02306 ENST00000546412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.8 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.538-2430G>T		intron_variant	Intron 5 of 9	3
LINC02306	ENST00000736904.1	n.280-2430G>T		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70515 AN: 151680 Hom.: 19368 Cov.: 31

Gnomad AFR AF: 0.721

Gnomad AMI AF: 0.244

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.820

Gnomad SAS AF: 0.602

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.315

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.465 AC: 70607 AN: 151798 Hom.: 19402 Cov.: 31 AF XY: 0.472 AC XY: 35004 AN XY: 74162

African (AFR) AF: 0.721 AC: 29814 AN: 41358

American (AMR) AF: 0.463 AC: 7074 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 984 AN: 3464

East Asian (EAS) AF: 0.821 AC: 4215 AN: 5134

South Asian (SAS) AF: 0.601 AC: 2888 AN: 4806

European-Finnish (FIN) AF: 0.373 AC: 3921 AN: 10522

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.302 AC: 20526 AN: 67940

Other (OTH) AF: 0.415 AC: 872 AN: 2102

Alfa AF: 0.356 Hom.: 32965

Bravo AF: 0.481

Asia WGS AF: 0.685 AC: 2379 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	0.011
DANN	Benign	0.29
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs1475010; hg19: chr14-26136611;