chr3-39482025-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001393704.1(MOBP):c.-5+1902C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 152,038 control chromosomes in the GnomAD database, including 13,436 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 ( 13436 hom., cov: 32)
Consequence
MOBP
NM_001393704.1 intron
NM_001393704.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.61
Publications
5 publications found
Genes affected
MOBP (HGNC:7189): (myelin associated oligodendrocyte basic protein) Predicted to enable actin binding activity and myosin binding activity. Predicted to be a structural constituent of myelin sheath. Predicted to be involved in nervous system development. Predicted to be located in mitochondrion. Predicted to be active in cortical actin cytoskeleton. Implicated in frontotemporal dementia. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.87).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MOBP | NM_001393704.1 | c.-5+1902C>T | intron_variant | Intron 2 of 3 | ENST00000684792.1 | NP_001380633.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.356 AC: 54068AN: 151920Hom.: 13395 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
54068
AN:
151920
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.356 AC: 54159AN: 152038Hom.: 13436 Cov.: 32 AF XY: 0.348 AC XY: 25901AN XY: 74326 show subpopulations
GnomAD4 genome
AF:
AC:
54159
AN:
152038
Hom.:
Cov.:
32
AF XY:
AC XY:
25901
AN XY:
74326
show subpopulations
African (AFR)
AF:
AC:
29304
AN:
41416
American (AMR)
AF:
AC:
3490
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
963
AN:
3468
East Asian (EAS)
AF:
AC:
1411
AN:
5174
South Asian (SAS)
AF:
AC:
1441
AN:
4826
European-Finnish (FIN)
AF:
AC:
1774
AN:
10584
Middle Eastern (MID)
AF:
AC:
95
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14817
AN:
67972
Other (OTH)
AF:
AC:
701
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1393
2786
4180
5573
6966
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
480
960
1440
1920
2400
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
1169
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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