chr8:38429736:C>T Detail (hg38) (FGFR1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr8:38,287,254-38,287,254 View the variant detail on this assembly version. |
| hg38 | chr8:38,429,736-38,429,736 |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_023106.2:c.92-1301G>A | |
| NM_001174064.1:c.280G>A | NP_001167535.1:p.Val94Ile | |
| NM_023105.2:c.92-1301G>A |
Summary
MGeND
| Clinical significance |
Pathogenic
|
| Variant entry | 1 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.007 |
| ToMMo:0.006 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.008 |
Prediction
ClinVar
| Clinical Significance |
Benign
Likely benign
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Pathogenic
|
hypogonadotropic hypogonadism with or without anosmia |
germline
|
MGS000001
(TMGS000138) |
Kenjiro Kosaki | Keio University |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2018-02-26 | criteria provided, single submitter | Hartsfield-Bixler-Demyer syndrome |
unknown
|
Detail |
|
Benign
|
2023-10-03 | criteria provided, single submitter | hypogonadotropic hypogonadism 2 with or without anosmia,Pfeiffer syndrome |
germline
|
Detail |
|
Benign
|
2023-10-03 | criteria provided, single submitter | hypogonadotropic hypogonadism 2 with or without anosmia,Pfeiffer syndrome |
germline
|
Detail |
|
Benign
|
2017-04-28 | criteria provided, single submitter | hypogonadotropic hypogonadism 2 with or without anosmia |
germline
|
Detail |
|
Benign
|
2017-04-28 | criteria provided, single submitter | Craniosynostosis syndrome |
germline
|
Detail |
|
Benign
|
2017-04-28 | criteria provided, single submitter | Trigonocephaly 1 |
germline
|
Detail |
|
Benign
|
2017-04-28 | criteria provided, single submitter | osteoglophonic dysplasia |
germline
|
Detail |
|
Likely benign
|
2020-11-17 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Likely benign
|
2020-03-09 | criteria provided, single submitter | FGFR1-related disorder |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.241 | Kallmann Syndrome 2 (disorder) | Kallmann syndrome: 14 novel mutations in KAL1 and FGFR1 (KAL2). | UNIPROT | 15605412 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_023110.3(FGFR1):c.304G>A (p.Val102Ile) AND Hartsfield-Bixler-Demyer syndrome | ClinVar | Detail |
| NM_023110.3(FGFR1):c.304G>A (p.Val102Ile) AND multiple conditions | ClinVar | Detail |
| NM_023110.3(FGFR1):c.304G>A (p.Val102Ile) AND multiple conditions | ClinVar | Detail |
| NM_023110.3(FGFR1):c.304G>A (p.Val102Ile) AND Hypogonadotropic hypogonadism 2 with or without anosmi... | ClinVar | Detail |
| NM_023110.3(FGFR1):c.304G>A (p.Val102Ile) AND Craniosynostosis syndrome | ClinVar | Detail |
| NM_023110.3(FGFR1):c.304G>A (p.Val102Ile) AND Trigonocephaly 1 | ClinVar | Detail |
| NM_023110.3(FGFR1):c.304G>A (p.Val102Ile) AND Osteoglophonic dysplasia | ClinVar | Detail |
| NM_023110.3(FGFR1):c.304G>A (p.Val102Ile) AND not provided | ClinVar | Detail |
| NM_023110.3(FGFR1):c.304G>A (p.Val102Ile) AND FGFR1-related disorder | ClinVar | Detail |
| Kallmann syndrome: 14 novel mutations in KAL1 and FGFR1 (KAL2). | 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
- rs55642501 dbSNP
- Genome
- hg38
- Position
- chr8:38,429,736-38,429,736
- Variant Type
- snv
- Reference Allele
- C
- Alternative Allele
- T
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1200
- Mean of sample read depth (HGVD)
- 47.02
- Standard deviation of sample read depth (HGVD)
- 25.02
- Number of reference allele (HGVD)
- 2382
- Number of alternative allele (HGVD)
- 18
- Allele Frequency (HGVD)
- 0.0075
- Gene Symbol (HGVD)
- FGFR1
- 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))
- rs55642501
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0063
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 105
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- Homozygous Counts in All Race (ExAC)
- 0
- East Asian Chromosome Counts (ExAC)
- 1962
- East Asian Allele Counts (ExAC)
- 15
- East Asian Heterozygous Counts (ExAC)
- 15
- East Asian Homozygous Counts (ExAC)
- 0
- East Asian Allele Frequency (ExAC)
- 0.00764525993883792
- Chromosome Counts in All Race (ExAC)
- 34556
- Allele Counts in All Race (ExAC)
- 30
- Heterozygous Counts in All Race (ExAC)
- 30
- Allele Frequency in All Race (ExAC)
- 8.681560365783077E-4
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