chr7:12269417:C>G Detail (hg19) (TMEM106B)

Information

Genome

Assembly Position
hg19 chr7:12,269,417-12,269,417
hg38 chr7:12,229,791-12,229,791 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_018374.3:c.554C>G NP_060844.2:p.Thr185Ser
NM_001134232.1:c.554C>G NP_001127704.1:p.Thr185Ser
Ensemble ENST00000396667.7:c.554C>G ENST00000396667.7:p.Thr185Ser
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.593
ToMMo:0.592
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.654

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 613413 OMIM
HGNC 22407 HGNC
Ensembl ENSG00000106460 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv28352330 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-31 criteria provided, single submitter not provided germline Detail
Benign 2021-09-10 criteria provided, single submitter Leukodystrophy, hypomyelinating, 16 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.006 motor neuron disease We assessed the genotype of 325 C9ORF72 expansion carriers (cohort 1), 586 FTD p... BeFree 24385136 Detail
<0.001 motor neuron disease We assessed the genotype of 325 C9ORF72 expansion carriers (cohort 1), 586 FTD p... BeFree 24385136 Detail
0.282 frontotemporal dementia We studied the p.T185S TMEM106B genetic variant previously implicated in frontot... BeFree 23742080 Detail
0.002 frontotemporal dementia TMEM106B p.T185S regulates TMEM106B protein levels: implications for frontotempo... BeFree 23742080 Detail
0.001 Pick Disease of the Brain TMEM106B p.T185S regulates TMEM106B protein levels: implications for frontotempo... BeFree 23742080 Detail
0.027 Pick Disease of the Brain We studied the p.T185S TMEM106B genetic variant previously implicated in frontot... BeFree 23742080 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001134232.2(TMEM106B):c.554C>G (p.Thr185Ser) AND not provided ClinVar Detail
NM_001134232.2(TMEM106B):c.554C>G (p.Thr185Ser) AND Leukodystrophy, hypomyelinating, 16 ClinVar Detail
We assessed the genotype of 325 C9ORF72 expansion carriers (cohort 1), 586 FTD patients lacking C9OR... DisGeNET Detail
We assessed the genotype of 325 C9ORF72 expansion carriers (cohort 1), 586 FTD patients lacking C9OR... DisGeNET Detail
We studied the p.T185S TMEM106B genetic variant previously implicated in frontotemporal dementia wit... DisGeNET Detail
TMEM106B p.T185S regulates TMEM106B protein levels: implications for frontotemporal dementia. DisGeNET Detail
TMEM106B p.T185S regulates TMEM106B protein levels: implications for frontotemporal dementia. DisGeNET Detail
We studied the p.T185S TMEM106B genetic variant previously implicated in frontotemporal dementia wit... 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
rs3173615 dbSNP
Genome
hg19
Position
chr7:12,269,417-12,269,417
Variant Type
snv
Reference Allele
C
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1208
Mean of sample read depth (HGVD)
84.22
Standard deviation of sample read depth (HGVD)
33.75
Number of reference allele (HGVD)
983
Number of alternative allele (HGVD)
1433
Allele Frequency (HGVD)
0.5931291390728477
Gene Symbol (HGVD)
TMEM106B
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))
rs3173615
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5923
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9925
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8626
East Asian Allele Counts (ExAC)
5640
East Asian Heterozygous Counts (ExAC)
1982
East Asian Homozygous Counts (ExAC)
1829
East Asian Allele Frequency (ExAC)
0.6538372362624624
Chromosome Counts in All Race (ExAC)
120918
Allele Counts in All Race (ExAC)
59438
Heterozygous Counts in All Race (ExAC)
28306
Homozygous Counts in All Race (ExAC)
15566
Allele Frequency in All Race (ExAC)
0.4915562612679667
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