chr19:51746706:G>T Detail (hg38) (FPR1)

Information

Genome

Assembly Position
hg19 chr19:52,249,959-52,249,959 View the variant detail on this assembly version.
hg38 chr19:51,746,706-51,746,706

HGVS

Type Transcript Protein
RefSeq NM_002029.3:c.289C>A NP_002020.1:p.Leu97Met
NM_001193306.1:c.289C>A NP_001180235.1:p.Leu97Met
Ensemble ENST00000304748.5:c.289C>A ENST00000304748.5:p.Leu97Met
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.090
ToMMo:0.089
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.075

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 136537 OMIM
HGNC 3826 HGNC
Ensembl ENSG00000171051 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv62551128 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-23 criteria provided, single submitter Gingival disorder germline Detail
Benign 2019-12-16 criteria provided, single submitter FPR1-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.011 macular degeneration Combined heterozygous risk alleles of CFH rs800292 GA and FPR1 rs78488639 CA wer... BeFree 25277308 Detail
0.480 age related macular degeneration Combined heterozygous risk alleles of CFH rs800292 GA and FPR1 rs78488639 CA wer... BeFree 25277308 Detail
0.267 age related macular degeneration Furthermore, FPR1 rs78488639 CA combining with HTRA1 rs11200638 and smoking was ... BeFree 25277308 Detail
0.005 macular degeneration Furthermore, FPR1 rs78488639 CA combining with HTRA1 rs11200638 and smoking was ... BeFree 25277308 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002029.4(FPR1):c.289C>A (p.Leu97Met) AND Gingival disorder ClinVar Detail
NM_002029.4(FPR1):c.289C>A (p.Leu97Met) AND FPR1-related disorder ClinVar Detail
Combined heterozygous risk alleles of CFH rs800292 GA and FPR1 rs78488639 CA were posed to PCV (P=2.... DisGeNET Detail
Combined heterozygous risk alleles of CFH rs800292 GA and FPR1 rs78488639 CA were posed to PCV (P=2.... DisGeNET Detail
Furthermore, FPR1 rs78488639 CA combining with HTRA1 rs11200638 and smoking was also predisposed ris... DisGeNET Detail
Furthermore, FPR1 rs78488639 CA combining with HTRA1 rs11200638 and smoking was also predisposed ris... 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
rs78488639 dbSNP
Genome
hg38
Position
chr19:51,746,706-51,746,706
Variant Type
snv
Reference Allele
G
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1209
Mean of sample read depth (HGVD)
88.83
Standard deviation of sample read depth (HGVD)
42.68
Number of reference allele (HGVD)
2200
Number of alternative allele (HGVD)
218
Allele Frequency (HGVD)
0.09015715467328371
Gene Symbol (HGVD)
FPR1
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))
rs78488639
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0889
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1490
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
651
East Asian Heterozygous Counts (ExAC)
593
East Asian Homozygous Counts (ExAC)
29
East Asian Allele Frequency (ExAC)
0.07526011560693642
Chromosome Counts in All Race (ExAC)
121408
Allele Counts in All Race (ExAC)
1054
Heterozygous Counts in All Race (ExAC)
988
Homozygous Counts in All Race (ExAC)
33
Allele Frequency in All Race (ExAC)
0.00868147074327886
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