chr19:48968563:G>A Detail (hg38) (FTL, GYS1)

Information

Genome

Assembly Position
hg19 chr19:49,471,820-49,471,820 View the variant detail on this assembly version.
hg38 chr19:48,968,563-48,968,563

HGVS

Type Transcript Protein
RefSeq NM_001161587.1:c.*725C>T
NM_002103.4:c.*725C>T
NR_027763.1:c.*725C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.023
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.047

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 138570 OMIM
HGNC 4706 HGNC
Ensembl ENSG00000104812 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62425499 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-06-14 criteria provided, single submitter Neuroferritinopathy germline Detail
Likely benign 2016-06-14 criteria provided, single submitter Glycogen storage disease due to muscle and heart glycogen synthase deficiency germline Detail
Benign 2016-06-14 criteria provided, single submitter Hereditary hyperferritinemia with congenital cataracts germline Detail
Benign 2021-05-12 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 5,10-Methylenetetrahydrofolate reductase deficiency With the aim to conclusively validate the strongest associations so far reported... BeFree 24521996 Detail
<0.001 5,10-Methylenetetrahydrofolate reductase deficiency With the aim to conclusively validate the strongest associations so far reported... BeFree 24521996 Detail
<0.001 5,10-Methylenetetrahydrofolate reductase deficiency With the aim to conclusively validate the strongest associations so far reported... BeFree 24521996 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002103.5(GYS1):c.*725C>T AND Neuroferritinopathy ClinVar Detail
NM_002103.5(GYS1):c.*725C>T AND Glycogen storage disease due to muscle and heart glycogen synthase d... ClinVar Detail
NM_002103.5(GYS1):c.*725C>T AND Hereditary hyperferritinemia with congenital cataracts ClinVar Detail
NM_002103.5(GYS1):c.*725C>T AND not provided ClinVar Detail
With the aim to conclusively validate the strongest associations so far reported, we selected the po... DisGeNET Detail
With the aim to conclusively validate the strongest associations so far reported, we selected the po... DisGeNET Detail
With the aim to conclusively validate the strongest associations so far reported, we selected the po... 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
rs1042265 dbSNP
Genome
hg38
Position
chr19:48,968,563-48,968,563
Variant Type
snv
Reference Allele
G
Alternative Allele
A
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))
rs1042265
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0229
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
384
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
170
East Asian Allele Counts (ExAC)
8
East Asian Heterozygous Counts (ExAC)
8
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.047058823529411764
Chromosome Counts in All Race (ExAC)
11670
Allele Counts in All Race (ExAC)
892
Heterozygous Counts in All Race (ExAC)
818
Homozygous Counts in All Race (ExAC)
37
Allele Frequency in All Race (ExAC)
0.07643530419880035
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