dbSNP rs12586774: LINC02306:n.928+486C>A (chr14-25660360-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0510

Publications

3 publications found

Variant links:

Genes affected

LINC02306 (HGNC:53225): (long intergenic non-protein coding RNA 2306)

LINC02306 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

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 link	n.928+486C>A		intron_variant	Intron 8 of 9	3
LINC02306	ENST00000736904.1 link	n.736+486C>A		intron_variant	Intron 6 of 6

Frequencies

GnomAD3 genomes

AF:

0.0429

AC:

6520

AN:

152040

Hom.:

761

Cov.:

show subpopulations

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.:

AF XY:

0.0478

AC XY:

3558

AN XY:

74382

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.0224

AC:

1522

AN:

68008

Other (OTH)

AF:

0.0446

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

256

513

769

1026

1282

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

172

258

344

430

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.3

(source)

DANN

Benign

0.55

PhyloP100

-0.051

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over