chr1:227069677:T>C Detail (hg19) (PSEN2)

Information

Genome

Assembly Position
hg19 chr1:227,069,677-227,069,677
hg38 chr1:226,881,976-226,881,976 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000447.2:c.69T>C NP_000438.2:p.Ala23=
NM_012486.2:c.69T>C NP_036618.2:p.Ala23=
Ensemble ENST00000366782.6:c.69T>C ENST00000366782.6:p.Ala23=
Summary

MGeND

Clinical significance Benign other
Variant entry 668
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.707
ToMMo:0.711
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.563

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 600759 OMIM
HGNC 9509 HGNC
Ensembl ENSG00000143801 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv5029972 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
other others(exclude AD, MCI and NC) germline MGS000010
(TMGS000013) 		Hiroshi Mori Osaka City University
other mild cognitive impairment germline MGS000010
(TMGS000013) 		Hiroshi Mori Osaka City University
other Alzheimer's disease germline MGS000010
(TMGS000013) 		Hiroshi Mori Osaka City University
other normal cognition germline MGS000010
(TMGS000013) 		Hiroshi Mori Osaka City University
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 2017-07-24 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2021-10-25 criteria provided, multiple submitters, no conflicts dilated cardiomyopathy 1V germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Alzheimer disease 4 germline Detail
Benign 2023-11-29 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000447.3(PSEN2):c.69T>C (p.Ala23=) AND not specified ClinVar Detail
NM_000447.3(PSEN2):c.69T>C (p.Ala23=) AND Dilated cardiomyopathy 1V ClinVar Detail
NM_000447.3(PSEN2):c.69T>C (p.Ala23=) AND Alzheimer disease 4 ClinVar Detail
NM_000447.3(PSEN2):c.69T>C (p.Ala23=) AND not provided ClinVar 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
rs11405 dbSNP
Genome
hg19
Position
chr1:227,069,677-227,069,677
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1190
Mean of sample read depth (HGVD)
46.09
Standard deviation of sample read depth (HGVD)
22.35
Number of reference allele (HGVD)
696
Number of alternative allele (HGVD)
1681
Allele Frequency (HGVD)
0.7071939419436264
Gene Symbol (HGVD)
PSEN2
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))
rs11405
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.7109
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
11915
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8632
East Asian Allele Counts (ExAC)
4856
East Asian Heterozygous Counts (ExAC)
2126
East Asian Homozygous Counts (ExAC)
1365
East Asian Allele Frequency (ExAC)
0.5625579240037072
Chromosome Counts in All Race (ExAC)
121288
Allele Counts in All Race (ExAC)
92221
Heterozygous Counts in All Race (ExAC)
21641
Homozygous Counts in All Race (ExAC)
35290
Allele Frequency in All Race (ExAC)
0.7603472726073478
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