chr4:109980955:A>T Detail (hg38) (EGF, LOC126807134)

Information

Genome

Assembly Position
hg19 chr4:110,902,111-110,902,111 View the variant detail on this assembly version.
hg38 chr4:109,980,955-109,980,955

HGVS

Type Transcript Protein
RefSeq NM_001963.5:c.2351A>T NP_001954.2:p.Asp784Val
NM_001178130.2:c.2351A>T NP_001171601.1:p.Asp784Val
NM_001178131.2:c.2225A>T NP_001171602.1:p.Asp742Val
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.224
ToMMo:0.216
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.192

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 131530 OMIM
HGNC 3229 HGNC
Ensembl ENSG00000138798 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv18234832 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-03-06 criteria provided, single submitter renal hypomagnesemia 4 germline Detail
Benign 2024-01-29 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.144 liver carcinoma Additionally, the haplotype T-G constructed by rs11569017 and rs4444903 of the E... BeFree 23790025 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001963.6(EGF):c.2351A>T (p.Asp784Val) AND Renal hypomagnesemia 4 ClinVar Detail
NM_001963.6(EGF):c.2351A>T (p.Asp784Val) AND not provided ClinVar Detail
Additionally, the haplotype T-G constructed by rs11569017 and rs4444903 of the EGF gene might increa... 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
rs11569017 dbSNP
Genome
hg38
Position
chr4:109,980,955-109,980,955
Variant Type
snv
Reference Allele
A
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
125.83
Standard deviation of sample read depth (HGVD)
57.34
Number of reference allele (HGVD)
1878
Number of alternative allele (HGVD)
542
Allele Frequency (HGVD)
0.22396694214876034
Gene Symbol (HGVD)
EGF
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))
rs11569017
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2162
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3624
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8652
East Asian Allele Counts (ExAC)
1661
East Asian Heterozygous Counts (ExAC)
1315
East Asian Homozygous Counts (ExAC)
173
East Asian Allele Frequency (ExAC)
0.19197873324086917
Chromosome Counts in All Race (ExAC)
121390
Allele Counts in All Race (ExAC)
8552
Heterozygous Counts in All Race (ExAC)
7736
Homozygous Counts in All Race (ExAC)
408
Allele Frequency in All Race (ExAC)
0.0704506137243595
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