chr14-25681304-C-T

Variant summary

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

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.509

Publications

2 publications found
Variant links:
Genes affected
LINC02306 (HGNC:53225): (long intergenic non-protein coding RNA 2306)

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=-0.91).
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
LINC02306ENST00000546412.2 linkn.538-16329G>A intron_variant Intron 5 of 9 3
LINC02306ENST00000736904.1 linkn.280-16329G>A intron_variant Intron 3 of 6

Frequencies

GnomAD3 genomes
AF:
0.348
AC:
52984
AN:
152056
Hom.:
11292
Cov.:
33
show subpopulations
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
show subpopulations
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
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1598
3195
4793
6390
7988
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
508
1016
1524
2032
2540
<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:
0.432
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

Publications

Other links and lift over

dbSNP: rs12893752; hg19: chr14-26150510; API