chr6:41159805:G>A Detail (hg38) (TREM2)

Information

Genome

Assembly Position
hg19 chr6:41,127,543-41,127,543 View the variant detail on this assembly version.
hg38 chr6:41,159,805-41,159,805

HGVS

Type Transcript Protein
RefSeq NM_001271821.1:c.469C>T NP_001258750.1:p.His157Tyr
NM_018965.3:c.469C>T NP_061838.1:p.His157Tyr
Ensemble ENST00000338469.3:c.469C>T ENST00000338469.3:p.His157Tyr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.002

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 605086 OMIM
HGNC 17761 HGNC
Ensembl ENSG00000095970 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv25091786 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2015-05-11 criteria provided, multiple submitters, no conflicts not specified germline Detail
Likely benign 2021-08-12 criteria provided, multiple submitters, no conflicts Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy 2 germline unknown Detail
Benign Likely benign 2024-01-31 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_018965.4(TREM2):c.469C>T (p.His157Tyr) AND not specified ClinVar Detail
NM_018965.4(TREM2):c.469C>T (p.His157Tyr) AND Polycystic lipomembranous osteodysplasia with sclerosi... ClinVar Detail
NM_018965.4(TREM2):c.469C>T (p.His157Tyr) AND not provided ClinVar 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
rs2234255 dbSNP
Genome
hg38
Position
chr6:41,159,805-41,159,805
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1198
Mean of sample read depth (HGVD)
41.56
Standard deviation of sample read depth (HGVD)
21.28
Number of reference allele (HGVD)
2395
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1736227045075126E-4
Gene Symbol (HGVD)
TREM2
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))
rs2234255
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0007
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
12
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8614
East Asian Allele Counts (ExAC)
17
East Asian Heterozygous Counts (ExAC)
17
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0019735314604132806
Chromosome Counts in All Race (ExAC)
121006
Allele Counts in All Race (ExAC)
437
Heterozygous Counts in All Race (ExAC)
429
Homozygous Counts in All Race (ExAC)
4
Allele Frequency in All Race (ExAC)
0.003611391170685751
Genome browser