chr18:57580104:C>A Detail (hg38) (FECH)

Information

Genome

Assembly Position
hg19 chr18:55,247,336-55,247,336 View the variant detail on this assembly version.
hg38 chr18:57,580,104-57,580,104

HGVS

Type Transcript Protein
RefSeq NM_000140.3:c.163G>T NP_000131.2:p.Gly55Cys
NM_001012515.2:c.-54G>T
Ensemble ENST00000262093.11:c.163G>T ENST00000262093.11:p.Gly55Cys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.005
ToMMo:0.007
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.016

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 612386 OMIM
HGNC 3647 HGNC
Ensembl ENSG00000066926 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv60152556 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2019-05-28 criteria provided, multiple submitters, no conflicts Protoporphyria, erythropoietic, 1 germline unknown Detail
Benign 2016-03-28 criteria provided, single submitter not specified germline Detail
Conflicting interpretations of pathogenicity 2024-03-01 criteria provided, conflicting interpretations not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.609 erythropoietic protoporphyria NA CLINVAR Detail
0.609 erythropoietic protoporphyria Human erythropoietic protoporphyria: two point mutations in the ferrochelatase g... UNIPROT 1755842 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000140.5(FECH):c.163G>T (p.Gly55Cys) AND Protoporphyria, erythropoietic, 1 ClinVar Detail
NM_000140.5(FECH):c.163G>T (p.Gly55Cys) AND not specified ClinVar Detail
NM_000140.5(FECH):c.163G>T (p.Gly55Cys) AND not provided ClinVar Detail
NA DisGeNET Detail
Human erythropoietic protoporphyria: two point mutations in the ferrochelatase gene. 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
rs3848519 dbSNP
Genome
hg38
Position
chr18:57,580,104-57,580,104
Variant Type
snv
Reference Allele
C
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
87.16
Standard deviation of sample read depth (HGVD)
36.63
Number of reference allele (HGVD)
2407
Number of alternative allele (HGVD)
13
Allele Frequency (HGVD)
0.005371900826446281
Gene Symbol (HGVD)
FECH
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))
rs3848519
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0074
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
124
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)
140
East Asian Heterozygous Counts (ExAC)
138
East Asian Homozygous Counts (ExAC)
1
East Asian Allele Frequency (ExAC)
0.01617749017795239
Chromosome Counts in All Race (ExAC)
121410
Allele Counts in All Race (ExAC)
2693
Heterozygous Counts in All Race (ExAC)
2584
Homozygous Counts in All Race (ExAC)
54
Allele Frequency in All Race (ExAC)
0.022181039453092827
Genome browser