chr17:44073889:A>G Detail (hg19) (MAPT)

Information

Genome

Assembly Position
hg19 chr17:44,073,889-44,073,889
hg38 chr17:45,996,523-45,996,523 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_016835.4:c.1857A>G NP_058519.3:p.Ala619=
NM_005910.5:c.681A>G NP_005901.2:p.Ala227=
NM_001203251.1:c.594A>G NP_001190180.1:p.Ala198=
Summary

MGeND

Clinical significance Benign
Variant entry 0
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 157140 OMIM
HGNC 6893 HGNC
Ensembl ENSG00000186868 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv57936957 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign 2018/05/23 Aged, 100 and over germline MGS000013
(TMGS000027) 		Hiroshi Mori Osaka City University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-08-11 criteria provided, single submitter not provided germline not provided Detail
Benign 2011-02-25 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2018-01-13 criteria provided, single submitter MAPT-Related Spectrum Disorders germline Detail
Benign 2024-02-01 criteria provided, single submitter frontotemporal dementia germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.195 Neurodegenerative Disorders We analyzed the allelic and genotype frequency of MAPT rs1052553, which has been... BeFree 23911736 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001377265.1(MAPT):c.1857A>G (p.Ala619=) AND not provided ClinVar Detail
NM_001377265.1(MAPT):c.1857A>G (p.Ala619=) AND not specified ClinVar Detail
NM_001377265.1(MAPT):c.1857A>G (p.Ala619=) AND MAPT-Related Spectrum Disorders ClinVar Detail
NM_001377265.1(MAPT):c.1857A>G (p.Ala619=) AND Frontotemporal dementia ClinVar Detail
We analyzed the allelic and genotype frequency of MAPT rs1052553, which has been associated with som... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs1052553 dbSNP
Genome
hg19
Position
chr17:44,073,889-44,073,889
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1208
Mean of sample read depth (HGVD)
145.73
Standard deviation of sample read depth (HGVD)
73.04
Number of reference allele (HGVD)
2413
Number of alternative allele (HGVD)
3
Allele Frequency (HGVD)
0.0012417218543046358
Gene Symbol (HGVD)
MAPT
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs1052553
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8538
East Asian Allele Counts (ExAC)
7
East Asian Heterozygous Counts (ExAC)
7
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
8.198641368001874E-4
Chromosome Counts in All Race (ExAC)
117528
Allele Counts in All Race (ExAC)
17136
Heterozygous Counts in All Race (ExAC)
13890
Homozygous Counts in All Race (ExAC)
1623
Allele Frequency in All Race (ExAC)
0.14580355319583418
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