rs12586774

Variant names:

• chr14-25660360-G-T
• rs12586774
• ENST00000546412.2:n.928+486C>A

Variant summary

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

The ENST00000546412.2(LINC02306):​n.928+486C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0429 in 152,158 control chromosomes in the GnomAD database, including 763 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 0.043 (763 hom., cov: 32)
• Consequence: LINC02306 ENST00000546412.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 3 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 = 0.473 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02306	ENST00000546412.2	TSL:3	n.928+486C>A		intron	N/A
	LINC02306	ENST00000736904.1		n.736+486C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0429 AC: 6520 AN: 152040 Hom.: 761 Cov.: 32

Gnomad AFR AF: 0.00881

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0474

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.159

Gnomad FIN AF: 0.0405

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0224

Gnomad OTH AF: 0.0441

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

GnomAD4 genome AF: 0.0429 AC: 6521 AN: 152158 Hom.: 763 Cov.: 32 AF XY: 0.0478 AC XY: 3558 AN XY: 74382

African (AFR) AF: 0.00879 AC: 365 AN: 41540

American (AMR) AF: 0.0471 AC: 720 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3466

East Asian (EAS) AF: 0.489 AC: 2508 AN: 5126

South Asian (SAS) AF: 0.160 AC: 770 AN: 4822

European-Finnish (FIN) AF: 0.0405 AC: 429 AN: 10604

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0224 AC: 1522 AN: 68008

Other (OTH) AF: 0.0446 AC: 94 AN: 2108

Alfa AF: 0.0394 Hom.: 449

Bravo AF: 0.0422

Asia WGS AF: 0.253 AC: 880 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	1.3
DANN	Benign	0.55
PhyloP100		-0.051

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs12586774;

hg19: chr14-26129566;