chr19:19219115:C>T Detail (hg38) (NCAN)

Information

Genome

Assembly Position
hg19 chr19:19,329,924-19,329,924 View the variant detail on this assembly version.
hg38 chr19:19,219,115-19,219,115

HGVS

Type Transcript Protein
RefSeq NM_004386.2:c.274C>T NP_004377.2:p.Pro92Ser
Ensemble ENST00000252575.11:c.274C>T ENST00000252575.11:p.Pro92Ser
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.048
ToMMo:0.048
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.067

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 600826 OMIM
HGNC 2465 HGNC
Ensembl ENSG00000130287 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv61528001 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 obesity By studying the genetic variants of obese Taiwanese children, we confirmed that ... BeFree 24477042 Detail
<0.001 Non-alcoholic Fatty Liver Disease By studying the genetic variants of obese Taiwanese children, we confirmed that ... BeFree 24477042 Detail
<0.001 Steatohepatitis We investigated whether ultrasound-measured HS, with and without increased level... BeFree 23416328 Detail
<0.001 Fatty Liver We investigated whether ultrasound-measured HS, with and without increased level... BeFree 23416328 Detail
<0.001 Steatohepatitis We investigated whether ultrasound-measured HS, with and without increased level... BeFree 23416328 Detail
<0.001 Non-alcoholic Fatty Liver Disease By studying the genetic variants of obese Taiwanese children, we confirmed that ... BeFree 24477042 Detail
0.001 Fatty Liver We investigated whether ultrasound-measured HS, with and without increased level... BeFree 23416328 Detail
<0.001 adrenoleukodystrophy The frequency of the NCAN rs2228603 T allele was significantly increased in pati... BeFree 24946282 Detail
<0.001 Liver Cirrhosis, Alcoholic The frequency of the NCAN rs2228603 T allele was significantly increased in pati... BeFree 24946282 Detail
<0.001 Steatohepatitis NCAN rs2228603[T] is a risk factor for liver inflammation and fibrosis, suggesti... BeFree 23594525 Detail
Annotation

Annotations

DescrptionSourceLinks
By studying the genetic variants of obese Taiwanese children, we confirmed that the genetic variants... DisGeNET Detail
By studying the genetic variants of obese Taiwanese children, we confirmed that the genetic variants... DisGeNET Detail
We investigated whether ultrasound-measured HS, with and without increased levels of alanine aminotr... DisGeNET Detail
We investigated whether ultrasound-measured HS, with and without increased levels of alanine aminotr... DisGeNET Detail
We investigated whether ultrasound-measured HS, with and without increased levels of alanine aminotr... DisGeNET Detail
By studying the genetic variants of obese Taiwanese children, we confirmed that the genetic variants... DisGeNET Detail
We investigated whether ultrasound-measured HS, with and without increased levels of alanine aminotr... DisGeNET Detail
The frequency of the NCAN rs2228603 T allele was significantly increased in patients with HCC due to... DisGeNET Detail
The frequency of the NCAN rs2228603 T allele was significantly increased in patients with HCC due to... DisGeNET Detail
NCAN rs2228603[T] is a risk factor for liver inflammation and fibrosis, suggesting that this locus i... 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
-
Genome
hg38
Position
chr19:19,219,115-19,219,115
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1205
Mean of sample read depth (HGVD)
66.35
Standard deviation of sample read depth (HGVD)
36.21
Number of reference allele (HGVD)
2295
Number of alternative allele (HGVD)
115
Allele Frequency (HGVD)
0.04771784232365145
Gene Symbol (HGVD)
NCAN
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))
rs2228603
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.048
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
805
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8590
East Asian Allele Counts (ExAC)
572
East Asian Heterozygous Counts (ExAC)
536
East Asian Homozygous Counts (ExAC)
18
East Asian Allele Frequency (ExAC)
0.06658905704307334
Chromosome Counts in All Race (ExAC)
118760
Allele Counts in All Race (ExAC)
7631
Heterozygous Counts in All Race (ExAC)
7025
Homozygous Counts in All Race (ExAC)
303
Allele Frequency in All Race (ExAC)
0.06425564163017851
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