chr19:48965830:T>C Detail (hg38) (FTL, GYS1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr19:49,469,087-49,469,087 View the variant detail on this assembly version. |
| hg38 | chr19:48,965,830-48,965,830 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000146.3:c.163T>C | NP_000137.2:p.Leu55= |
| Ensemble | ENST00000331825.11:c.163T>C | ENST00000331825.11:p.Leu55= |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.419 |
| ToMMo:0.408 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.426 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000151) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Likely pathogenic
|
2014-09-21 | no assertion criteria provided | sporadic abdominal aortic aneurysm |
unknown
|
Detail |
|
Benign
|
2013-08-15 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2021-08-10 | criteria provided, multiple submitters, no conflicts | Neuroferritinopathy |
germline
|
Detail |
|
Benign
|
2021-08-10 | criteria provided, multiple submitters, no conflicts | Hereditary hyperferritinemia with congenital cataracts |
germline
unknown
|
Detail |
|
Benign
|
2016-06-14 | criteria provided, single submitter | Glycogen storage disease due to muscle and heart glycogen synthase deficiency |
germline
|
Detail |
|
Benign
|
2018-03-24 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2024-01-31 | criteria provided, single submitter | Hereditary hyperferritinemia with congenital cataracts,Neuroferritinopathy |
germline
|
Detail |
|
Benign
|
2024-01-31 | criteria provided, single submitter | Hereditary hyperferritinemia with congenital cataracts,Neuroferritinopathy |
germline
|
Detail |
|
Benign
|
2021-08-10 | criteria provided, single submitter | L-ferritin deficiency |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.003 | Hereditary hemochromatosis | Our results make it likely the role of rs10421768, rs235756, rs2230267 and rs143... | BeFree | 25976471 | Detail |
| <0.001 | Hereditary hemochromatosis | We investigated 6 polymorphisms (rs10421768 in HAMP gene, rs235756 in BMP2 gene,... | BeFree | 25976471 | Detail |
| 0.125 | Hereditary hemochromatosis | We investigated 6 polymorphisms (rs10421768 in HAMP gene, rs235756 in BMP2 gene,... | BeFree | 25976471 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000146.4(FTL):c.163T>C (p.Leu55=) AND sporadic abdominal aortic aneurysm | ClinVar | Detail |
| NM_000146.4(FTL):c.163T>C (p.Leu55=) AND not specified | ClinVar | Detail |
| NM_000146.4(FTL):c.163T>C (p.Leu55=) AND Neuroferritinopathy | ClinVar | Detail |
| NM_000146.4(FTL):c.163T>C (p.Leu55=) AND Hereditary hyperferritinemia with congenital cataracts | ClinVar | Detail |
| NM_000146.4(FTL):c.163T>C (p.Leu55=) AND Glycogen storage disease due to muscle and heart glycogen s... | ClinVar | Detail |
| NM_000146.4(FTL):c.163T>C (p.Leu55=) AND not provided | ClinVar | Detail |
| NM_000146.4(FTL):c.163T>C (p.Leu55=) AND multiple conditions | ClinVar | Detail |
| NM_000146.4(FTL):c.163T>C (p.Leu55=) AND multiple conditions | ClinVar | Detail |
| NM_000146.4(FTL):c.163T>C (p.Leu55=) AND L-ferritin deficiency | ClinVar | Detail |
| Our results make it likely the role of rs10421768, rs235756, rs2230267 and rs1439816 polymorphisms, ... | DisGeNET | Detail |
| We investigated 6 polymorphisms (rs10421768 in HAMP gene, rs235756 in BMP2 gene, rs2230267 in FTL ge... | DisGeNET | Detail |
| We investigated 6 polymorphisms (rs10421768 in HAMP gene, rs235756 in BMP2 gene, rs2230267 in FTL ge... | 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
- rs2230267 dbSNP
- Genome
- hg38
- Position
- chr19:48,965,830-48,965,830
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1209
- Mean of sample read depth (HGVD)
- 141.67
- Standard deviation of sample read depth (HGVD)
- 67.77
- Number of reference allele (HGVD)
- 1406
- Number of alternative allele (HGVD)
- 1012
- Allele Frequency (HGVD)
- 0.4185277088502895
- Gene Symbol (HGVD)
- FTL
- 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))
- rs2230267
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.4082
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 6842
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8634
- East Asian Allele Counts (ExAC)
- 3676
- East Asian Heterozygous Counts (ExAC)
- 2098
- East Asian Homozygous Counts (ExAC)
- 789
- East Asian Allele Frequency (ExAC)
- 0.4257586286773222
- Chromosome Counts in All Race (ExAC)
- 121252
- Allele Counts in All Race (ExAC)
- 60373
- Heterozygous Counts in All Race (ExAC)
- 29805
- Homozygous Counts in All Race (ExAC)
- 15284
- Allele Frequency in All Race (ExAC)
- 0.4979134364793983
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