ENST00000546412.2:n.538-10630G>T

Variant names:

• chr14-25675605-C-A
• rs8181969
• ENST00000546412.2:n.538-10630G>T

Variant summary

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

The ENST00000546412.2(LINC02306):​n.538-10630G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,024 control chromosomes in the GnomAD database, including 11,009 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 0.36 (11009 hom., cov: 33)
• Consequence: LINC02306 ENST00000546412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.781 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02306	ENST00000546412.2	TSL:3	n.538-10630G>T		intron	N/A
	LINC02306	ENST00000736904.1		n.280-10630G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55248 AN: 151906 Hom.: 11005 Cov.: 33

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.801

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.364 AC: 55282 AN: 152024 Hom.: 11009 Cov.: 33 AF XY: 0.374 AC XY: 27779 AN XY: 74304

African (AFR) AF: 0.370 AC: 15323 AN: 41454

American (AMR) AF: 0.422 AC: 6453 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 925 AN: 3464

East Asian (EAS) AF: 0.802 AC: 4139 AN: 5162

South Asian (SAS) AF: 0.600 AC: 2890 AN: 4816

European-Finnish (FIN) AF: 0.365 AC: 3858 AN: 10560

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20685 AN: 67970

Other (OTH) AF: 0.337 AC: 711 AN: 2112

Alfa AF: 0.322 Hom.: 13805

Bravo AF: 0.365

Asia WGS AF: 0.654 AC: 2272 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.55
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs8181969; hg19: chr14-26144811;