chr17:78081415:C>T Detail (hg19) (GAA)

Information

Genome

Assembly Position
hg19 chr17:78,081,415-78,081,415
hg38 chr17:80,107,616-80,107,616 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001079803.2:c.752C>T NP_001073271.1:p.Ser251Leu
NM_001079804.2:c.752C>T NP_001073272.1:p.Ser251Leu
NM_000152.4:c.752C>T NP_000143.2:p.Ser251Leu
Summary

MGeND

Clinical significance Pathogenic
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.004
ToMMo:0.002
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.003

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 606800 OMIM
HGNC 4065 HGNC
Ensembl ENSG00000171298 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv58857485 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic other germline MGS000067
(TMGS000139) 		Kenjiro Kosaki Keio University
Pathogenic other germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Conflicting interpretations of pathogenicity 2022-09-27 criteria provided, conflicting interpretations Glycogen storage disease, type II germline unknown Detail
Conflicting interpretations of pathogenicity 2022-11-22 criteria provided, conflicting interpretations not provided germline Detail
Pathogenic 2022-12-05 criteria provided, single submitter Glycogen storage disease, type II germline Detail
Uncertain significance 2022-05-02 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.499 Glycogen storage disease type II Therefore, newborn screening for Pompe disease could be successfully conducted b... UNIPROT 20080426 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000152.5(GAA):c.752C>T (p.Ser251Leu) AND Glycogen storage disease, type II ClinVar Detail
NM_000152.5(GAA):c.752C>T (p.Ser251Leu) AND not provided ClinVar Detail
NM_000152.5(GAA):c.[752C>T;761C>T] AND Glycogen storage disease, type II ClinVar Detail
NM_000152.5(GAA):c.752C>T (p.Ser251Leu) AND not specified ClinVar Detail
Therefore, newborn screening for Pompe disease could be successfully conducted by including genotypi... 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
rs200856561 dbSNP
Genome
hg19
Position
chr17:78,081,415-78,081,415
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1208
Mean of sample read depth (HGVD)
118.30
Standard deviation of sample read depth (HGVD)
56.94
Number of reference allele (HGVD)
2406
Number of alternative allele (HGVD)
10
Allele Frequency (HGVD)
0.0041390728476821195
Gene Symbol (HGVD)
GAA
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))
rs200856561
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0018
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
31
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8622
East Asian Allele Counts (ExAC)
25
East Asian Heterozygous Counts (ExAC)
25
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.002899559266991417
Chromosome Counts in All Race (ExAC)
120654
Allele Counts in All Race (ExAC)
36
Heterozygous Counts in All Race (ExAC)
36
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
2.983738624496494E-4
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