chr3:172165727:C>T Detail (hg19) (GHSR)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr3:172,165,727-172,165,727 |
| hg38 | chr3:172,447,937-172,447,937 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_198407.2:c.477G>A | NP_940799.1:p.Arg159= |
| NM_004122.2:c.477G>A | NP_004113.1:p.Arg159= | |
| Ensemble | ENST00000241256.3:c.477G>A | ENST00000241256.3:p.Arg159= |
Summary
MGeND
| Clinical significance | |
| Variant entry | |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.412 |
| ToMMo:0.414 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.469 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
criteria provided, single submitter | not specified |
germline
|
Detail | |
|
Benign
|
2021-08-10 | criteria provided, multiple submitters, no conflicts | Short stature due to growth hormone secretagogue receptor deficiency |
germline
|
Detail |
|
Benign
|
2024-01-31 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.440 | obesity | Therefore, the present study aimed to evaluate the relationships among the gene ... | BeFree | 26255942 | Detail |
| 0.151 | obesity | Therefore, the present study aimed to evaluate the relationships among the gene ... | BeFree | 26255942 | Detail |
| 0.013 | obesity | Therefore, the present study aimed to evaluate the relationships among the gene ... | BeFree | 26255942 | Detail |
| 0.641 | obesity | Therefore, the present study aimed to evaluate the relationships among the gene ... | BeFree | 26255942 | Detail |
| 0.008 | Malignant neoplasm of breast | This study suggests that the rs696217 and rs2075356 ghrelin gene (GHRL) polymorp... | BeFree | 25376984 | Detail |
| 0.001 | breast carcinoma | This study suggests that the rs696217 and rs2075356 ghrelin gene (GHRL) polymorp... | BeFree | 25376984 | Detail |
| 0.006 | Malignant neoplasm of breast | This study suggests that the rs696217 and rs2075356 ghrelin gene (GHRL) polymorp... | BeFree | 25376984 | Detail |
| <0.001 | breast carcinoma | This study suggests that the rs696217 and rs2075356 ghrelin gene (GHRL) polymorp... | BeFree | 25376984 | Detail |
| <0.001 | obesity | In the obesity case-control study, the GHSR SNP rs572169 was found to be associa... | BeFree | 19165163 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_198407.2(GHSR):c.477G>A (p.Arg159=) AND not specified | ClinVar | Detail |
| NM_198407.2(GHSR):c.477G>A (p.Arg159=) AND Short stature due to growth hormone secretagogue receptor... | ClinVar | Detail |
| NM_198407.2(GHSR):c.477G>A (p.Arg159=) AND not provided | ClinVar | Detail |
| Therefore, the present study aimed to evaluate the relationships among the gene polymorphisms ghreli... | DisGeNET | Detail |
| Therefore, the present study aimed to evaluate the relationships among the gene polymorphisms ghreli... | DisGeNET | Detail |
| Therefore, the present study aimed to evaluate the relationships among the gene polymorphisms ghreli... | DisGeNET | Detail |
| Therefore, the present study aimed to evaluate the relationships among the gene polymorphisms ghreli... | DisGeNET | Detail |
| This study suggests that the rs696217 and rs2075356 ghrelin gene (GHRL) polymorphisms may protect ca... | DisGeNET | Detail |
| This study suggests that the rs696217 and rs2075356 ghrelin gene (GHRL) polymorphisms may protect ca... | DisGeNET | Detail |
| This study suggests that the rs696217 and rs2075356 ghrelin gene (GHRL) polymorphisms may protect ca... | DisGeNET | Detail |
| This study suggests that the rs696217 and rs2075356 ghrelin gene (GHRL) polymorphisms may protect ca... | DisGeNET | Detail |
| In the obesity case-control study, the GHSR SNP rs572169 was found to be associated with obesity (P ... | 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
- rs572169 dbSNP
- Genome
- hg19
- Position
- chr3:172,165,727-172,165,727
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1199
- Mean of sample read depth (HGVD)
- 58.16
- Standard deviation of sample read depth (HGVD)
- 30.64
- Number of reference allele (HGVD)
- 1409
- Number of alternative allele (HGVD)
- 989
- Allele Frequency (HGVD)
- 0.4124270225187656
- Gene Symbol (HGVD)
- GHSR
- 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))
- rs572169
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.4137
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 6933
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8616
- East Asian Allele Counts (ExAC)
- 4039
- East Asian Heterozygous Counts (ExAC)
- 2143
- East Asian Homozygous Counts (ExAC)
- 948
- East Asian Allele Frequency (ExAC)
- 0.4687790157845868
- Chromosome Counts in All Race (ExAC)
- 120576
- Allele Counts in All Race (ExAC)
- 36386
- Heterozygous Counts in All Race (ExAC)
- 24216
- Homozygous Counts in All Race (ExAC)
- 6085
- Allele Frequency in All Race (ExAC)
- 0.30176817940552014
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