chr18:57580222:G>A Detail (hg38) (FECH, LOC130062555)

Information

Genome

Assembly Position
hg19 chr18:55,247,454-55,247,454 View the variant detail on this assembly version.
hg38 chr18:57,580,222-57,580,222

HGVS

Type Transcript Protein
RefSeq NM_000140.3:c.68-23C>T
NM_001012515.2:c.-149-23C>T
Ensemble ENST00000262093.11:c.68-23C>T
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.385
ToMMo:0.416
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.309

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 tgv60152577 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Conflicting interpretations of pathogenicity 2021-12-08 criteria provided, conflicting interpretations Protoporphyria, erythropoietic, 1 germline unknown Detail
Likely benign 2016-01-25 no assertion criteria provided unknown Detail
Benign 2024-01-24 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.609 erythropoietic protoporphyria NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000140.5(FECH):c.68-23C>T AND Protoporphyria, erythropoietic, 1 ClinVar Detail
NM_000140.5(FECH):c.68-23C>T AND multiple conditions ClinVar Detail
NM_000140.5(FECH):c.68-23C>T AND not provided ClinVar Detail
NA DisGeNET Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2269219 dbSNP
Genome
hg38
Position
chr18:57,580,222-57,580,222
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
837
Mean of sample read depth (HGVD)
33.76
Standard deviation of sample read depth (HGVD)
11.74
Number of reference allele (HGVD)
1030
Number of alternative allele (HGVD)
644
Allele Frequency (HGVD)
0.3847072879330944
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))
rs2269219
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4162
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6975
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8584
East Asian Allele Counts (ExAC)
2655
East Asian Heterozygous Counts (ExAC)
1843
East Asian Homozygous Counts (ExAC)
406
East Asian Allele Frequency (ExAC)
0.3092963653308481
Chromosome Counts in All Race (ExAC)
120766
Allele Counts in All Race (ExAC)
29792
Heterozygous Counts in All Race (ExAC)
21070
Homozygous Counts in All Race (ExAC)
4361
Allele Frequency in All Race (ExAC)
0.24669194972094796
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