chr8:11643553:G>T Detail (hg19) (NEIL2)

Information

Genome

Assembly Position
hg19 chr8:11,643,553-11,643,553
hg38 chr8:11,786,044-11,786,044 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_145043.2:c.770G>T NP_659480.1:p.Arg257Leu
NM_001135747.1:c.587G>T NP_001129219.1:p.Arg196Leu
NM_001135746.1:c.770G>T NP_001129218.1:p.Arg257Leu
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.211
ToMMo:0.231
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.224

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 608933 OMIM
HGNC 18956 HGNC
Ensembl ENSG00000154328 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv32126753 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 Impaired cognition Dispersed association effects involving MutYH(His324Gln), MutYH(Met22Val), PolB(... BeFree 21884718 Detail
<0.001 Impaired cognition Dispersed association effects involving MutYH(His324Gln), MutYH(Met22Val), PolB(... BeFree 21884718 Detail
Annotation

Annotations

DescrptionSourceLinks
Dispersed association effects involving MutYH(His324Gln), MutYH(Met22Val), PolB(Pro242Arg) and NEIL2... DisGeNET Detail
Dispersed association effects involving MutYH(His324Gln), MutYH(Met22Val), PolB(Pro242Arg) and NEIL2... 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
hg19
Position
chr8:11,643,553-11,643,553
Variant Type
snv
Reference Allele
G
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1018
Mean of sample read depth (HGVD)
26.56
Standard deviation of sample read depth (HGVD)
25.50
Number of reference allele (HGVD)
1607
Number of alternative allele (HGVD)
429
Allele Frequency (HGVD)
0.2107072691552063
Gene Symbol (HGVD)
NEIL2
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))
rs8191664
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2314
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3878
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8644
East Asian Allele Counts (ExAC)
1939
East Asian Heterozygous Counts (ExAC)
1497
East Asian Homozygous Counts (ExAC)
221
East Asian Allele Frequency (ExAC)
0.22431744562702452
Chromosome Counts in All Race (ExAC)
121302
Allele Counts in All Race (ExAC)
4421
Heterozygous Counts in All Race (ExAC)
3857
Homozygous Counts in All Race (ExAC)
282
Allele Frequency in All Race (ExAC)
0.0364462251240705
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