chr21:25891809:G>A Detail (hg38) (APP)

Information

Genome

Assembly Position
hg19 chr21:27,264,121-27,264,121 View the variant detail on this assembly version.
hg38 chr21:25,891,809-25,891,809

HGVS

Type Transcript Protein
RefSeq NM_000484.3:c.2124C>T NP_000475.1:p.Gly708=
NM_001204303.1:c.1899C>T NP_001191232.1:p.Gly633=
NM_201414.2:c.1899C>T NP_958817.1:p.Gly633=
Summary

MGeND

Clinical significance
Variant entry
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 Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 104760 OMIM
HGNC 620 HGNC
Ensembl ENSG00000142192 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv64716160 TogoVar
COSMIC COSM1413495 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 1992-07-01 no assertion criteria provided APP POLYMORPHISM germline Detail
Benign Likely benign 2023-11-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign Likely benign 2024-01-25 criteria provided, multiple submitters, no conflicts Alzheimer disease germline Detail
Benign no assertion criteria provided not specified germline Detail
Likely benign 2021-07-29 criteria provided, single submitter Cerebral amyloid angiopathy, APP-related,Alzheimer disease type 1 unknown Detail
Likely benign 2021-07-29 criteria provided, single submitter Cerebral amyloid angiopathy, APP-related,Alzheimer disease type 1 unknown Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000484.4(APP):c.2124C>T (p.Gly708=) AND APP POLYMORPHISM ClinVar Detail
NM_000484.4(APP):c.2124C>T (p.Gly708=) AND not provided ClinVar Detail
NM_000484.4(APP):c.2124C>T (p.Gly708=) AND Alzheimer disease ClinVar Detail
NM_000484.4(APP):c.2124C>T (p.Gly708=) AND not specified ClinVar Detail
NM_000484.4(APP):c.2124C>T (p.Gly708=) AND multiple conditions ClinVar Detail
NM_000484.4(APP):c.2124C>T (p.Gly708=) AND multiple conditions 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
rs148888161 dbSNP
Genome
hg38
Position
chr21:25,891,809-25,891,809
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
100.04
Standard deviation of sample read depth (HGVD)
45.71
Number of reference allele (HGVD)
2419
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1322314049586776E-4
Gene Symbol (HGVD)
APP
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))
rs148888161
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8646
East Asian Allele Counts (ExAC)
12
East Asian Heterozygous Counts (ExAC)
12
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0013879250520471894
Chromosome Counts in All Race (ExAC)
121330
Allele Counts in All Race (ExAC)
248
Heterozygous Counts in All Race (ExAC)
248
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
0.0020440121981373117
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