chr10:71332204:A>G Detail (hg19) (NEUROG3)

Information

Genome

Assembly Position
hg19 chr10:71,332,204-71,332,204
hg38 chr10:69,572,448-69,572,448 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_020999.3:c.596T>C NP_066279.2:p.Phe199Ser
Ensemble ENST00000242462.5:c.596T>C ENST00000242462.5:p.Phe199Ser
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.287
ToMMo:0.286
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.366

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 604882 OMIM
HGNC 13806 HGNC
Ensembl ENSG00000122859 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv39666773 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-03-29 criteria provided, single submitter not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2021-09-05 criteria provided, single submitter congenital malabsorptive diarrhea 4 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.016 Diabetes Mellitus, Non-Insulin-Dependent Polymorphisms of these genes (Ala45Thr [NEUROD1], Ser199Phe [NEUROG3], and Ala98... BeFree 15277395 Detail
0.283 Diabetes Mellitus, Non-Insulin-Dependent Polymorphisms of these genes (Ala45Thr [NEUROD1], Ser199Phe [NEUROG3], and Ala98... BeFree 15277395 Detail
0.329 Diabetes Mellitus, Non-Insulin-Dependent Polymorphisms of these genes (Ala45Thr [NEUROD1], Ser199Phe [NEUROG3], and Ala98... BeFree 15277395 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_020999.4(NEUROG3):c.596T>C (p.Phe199Ser) AND not specified ClinVar Detail
NM_020999.4(NEUROG3):c.596T>C (p.Phe199Ser) AND not provided ClinVar Detail
NM_020999.4(NEUROG3):c.596T>C (p.Phe199Ser) AND Congenital malabsorptive diarrhea 4 ClinVar Detail
Polymorphisms of these genes (Ala45Thr [NEUROD1], Ser199Phe [NEUROG3], and Ala98Val [TCF1]) have bee... DisGeNET Detail
Polymorphisms of these genes (Ala45Thr [NEUROD1], Ser199Phe [NEUROG3], and Ala98Val [TCF1]) have bee... DisGeNET Detail
Polymorphisms of these genes (Ala45Thr [NEUROD1], Ser199Phe [NEUROG3], and Ala98Val [TCF1]) have bee... 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
rs4536103 dbSNP
Genome
hg19
Position
chr10:71,332,204-71,332,204
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1183
Mean of sample read depth (HGVD)
173.71
Standard deviation of sample read depth (HGVD)
80.90
Number of reference allele (HGVD)
1688
Number of alternative allele (HGVD)
678
Allele Frequency (HGVD)
0.2865595942519019
Gene Symbol (HGVD)
NEUROG3
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))
rs4536103
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2864
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4799
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
4120
East Asian Allele Counts (ExAC)
1506
East Asian Heterozygous Counts (ExAC)
1130
East Asian Homozygous Counts (ExAC)
188
East Asian Allele Frequency (ExAC)
0.3655339805825243
Chromosome Counts in All Race (ExAC)
69432
Allele Counts in All Race (ExAC)
40686
Heterozygous Counts in All Race (ExAC)
17962
Homozygous Counts in All Race (ExAC)
11362
Allele Frequency in All Race (ExAC)
0.5859834082267542
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