rs12150242
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001377265.1(MAPT):c.-17-23871A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,218 control chromosomes in the GnomAD database, including 2,135 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 0.14 ( 2135 hom., cov: 32)
Consequence
MAPT
NM_001377265.1 intron
NM_001377265.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.218
Publications
19 publications found
Genes affected
MAPT (HGNC:6893): (microtubule associated protein tau) This gene encodes the microtubule-associated protein tau (MAPT) whose transcript undergoes complex, regulated alternative splicing, giving rise to several mRNA species. MAPT transcripts are differentially expressed in the nervous system, depending on stage of neuronal maturation and neuron type. MAPT gene mutations have been associated with several neurodegenerative disorders such as Alzheimer's disease, Pick's disease, frontotemporal dementia, cortico-basal degeneration and progressive supranuclear palsy. [provided by RefSeq, Jul 2008]
MAPT Gene-Disease associations (from GenCC):
- Pick diseaseInheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp
- semantic dementiaInheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
- supranuclear palsy, progressive, 1Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
- late-onset Parkinson diseaseInheritance: Unknown, AD Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp
- progressive supranuclear palsy-parkinsonism syndromeInheritance: AR Classification: MODERATE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), Genomics England PanelApp
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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=-0.98).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAPT | NM_001377265.1 | c.-17-23871A>G | intron_variant | Intron 1 of 12 | ENST00000262410.10 | NP_001364194.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAPT | ENST00000262410.10 | c.-17-23871A>G | intron_variant | Intron 1 of 12 | 1 | NM_001377265.1 | ENSP00000262410.6 |
Frequencies
GnomAD3 genomes AF: 0.144 AC: 21832AN: 152100Hom.: 2137 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
21832
AN:
152100
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: 0.143 AC: 21822AN: 152218Hom.: 2135 Cov.: 32 AF XY: 0.134 AC XY: 9982AN XY: 74434 show subpopulations
GnomAD4 genome
AF:
AC:
21822
AN:
152218
Hom.:
Cov.:
32
AF XY:
AC XY:
9982
AN XY:
74434
show subpopulations
African (AFR)
AF:
AC:
1787
AN:
41552
American (AMR)
AF:
AC:
2683
AN:
15290
Ashkenazi Jewish (ASJ)
AF:
AC:
836
AN:
3470
East Asian (EAS)
AF:
AC:
8
AN:
5186
South Asian (SAS)
AF:
AC:
356
AN:
4818
European-Finnish (FIN)
AF:
AC:
689
AN:
10602
Middle Eastern (MID)
AF:
AC:
64
AN:
294
European-Non Finnish (NFE)
AF:
AC:
14762
AN:
67982
Other (OTH)
AF:
AC:
384
AN:
2112
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
946
1891
2837
3782
4728
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
234
468
702
936
1170
<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:
109
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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