ENST00000658247.1:n.363+40469A>C

Variant summary

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

The ENST00000658247.1(LINC00378):​n.363+40469A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,952 control chromosomes in the GnomAD database, including 21,862 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 0.52 ( 21862 hom., cov: 31)

Consequence

LINC00378
ENST00000658247.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

1 publications found
Variant links:
Genes affected
LINC00378 (HGNC:42704): (long intergenic non-protein coding RNA 378)

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=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.875 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
LINC00378ENST00000658247.1 linkn.363+40469A>C intron_variant Intron 3 of 4

Frequencies

GnomAD3 genomes
AF:
0.524
AC:
79501
AN:
151834
Hom.:
21860
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.381
Gnomad AMI
AF:
0.480
Gnomad AMR
AF:
0.614
Gnomad ASJ
AF:
0.565
Gnomad EAS
AF:
0.896
Gnomad SAS
AF:
0.515
Gnomad FIN
AF:
0.559
Gnomad MID
AF:
0.652
Gnomad NFE
AF:
0.553
Gnomad OTH
AF:
0.576
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.523
AC:
79546
AN:
151952
Hom.:
21862
Cov.:
31
AF XY:
0.525
AC XY:
38950
AN XY:
74242
show subpopulations
African (AFR)
AF:
0.380
AC:
15756
AN:
41428
American (AMR)
AF:
0.614
AC:
9375
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.565
AC:
1959
AN:
3470
East Asian (EAS)
AF:
0.896
AC:
4631
AN:
5166
South Asian (SAS)
AF:
0.516
AC:
2481
AN:
4810
European-Finnish (FIN)
AF:
0.559
AC:
5909
AN:
10570
Middle Eastern (MID)
AF:
0.653
AC:
192
AN:
294
European-Non Finnish (NFE)
AF:
0.553
AC:
37586
AN:
67930
Other (OTH)
AF:
0.578
AC:
1219
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.510
Heterozygous variant carriers
0
1889
3777
5666
7554
9443
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
686
1372
2058
2744
3430
<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:
0.534
Hom.:
13364
Bravo
AF:
0.527
Asia WGS
AF:
0.713
AC:
2472
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.37
DANN
Benign
0.44
PhyloP100
-1.1

Splicing

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

Publications

Other links and lift over

dbSNP: rs4886286; hg19: chr13-61465129; API