chr2:21238034:T>C Detail (hg19) (APOB)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr2:21,238,034-21,238,034 |
| hg38 | chr2:21,015,162-21,015,162 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000384.2:c.3607A>G | NP_000375.2:p.Ser1203Gly |
| Ensemble | ENST00000233242.5:c.3607A>G | ENST00000233242.5:p.Ser1203Gly |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 1 |
| 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:0.002 |
Prediction
ClinVar
| Clinical Significance | Conflicting classifications of pathogenicity |
| 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
(TMGS000140) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
Uncertain significance
|
2022-05-24 | criteria provided, single submitter | not provided |
germline
|
Detail |
Likely benign
|
2024-01-21 | criteria provided, single submitter | familial hypobetalipoproteinemia 1,Hypercholesterolemia, autosomal dominant, type B |
germline
|
Detail |
|
Likely benign
|
2024-01-21 | criteria provided, single submitter | familial hypobetalipoproteinemia 1,Hypercholesterolemia, autosomal dominant, type B |
germline
|
Detail |
|
Likely benign
|
2023-11-03 | criteria provided, single submitter |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000384.3(APOB):c.3607A>G (p.Ser1203Gly) AND not provided | ClinVar | Detail |
| NM_000384.3(APOB):c.3607A>G (p.Ser1203Gly) AND multiple conditions | ClinVar | Detail |
| NM_000384.3(APOB):c.3607A>G (p.Ser1203Gly) AND multiple conditions | ClinVar | Detail |
| NM_000384.3(APOB):c.3607A>G (p.Ser1203Gly) AND Cardiovascular phenotype | 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
- rs78875649 dbSNP
- Genome
- hg19
- Position
- chr2:21,238,034-21,238,034
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1208
- Mean of sample read depth (HGVD)
- 53.62
- Standard deviation of sample read depth (HGVD)
- 30.17
- Number of reference allele (HGVD)
- 2414
- Number of alternative allele (HGVD)
- 2
- Allele Frequency (HGVD)
- 8.278145695364238E-4
- Gene Symbol (HGVD)
- APOB
- 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))
- rs78875649
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0012
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 20
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8654
- East Asian Allele Counts (ExAC)
- 13
- East Asian Heterozygous Counts (ExAC)
- 13
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.0015021955165241507
- Chromosome Counts in All Race (ExAC)
- 121406
- Allele Counts in All Race (ExAC)
- 13
- Heterozygous Counts in All Race (ExAC)
- 13
- Homozygous Counts in All Race (ExAC)
- 0
- Allele Frequency in All Race (ExAC)
- 1.070787275752434E-4
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