chr16:2125834:T>C Detail (hg19) (TSC2)

Information

Genome

Assembly Position
hg19 chr16:2,125,834-2,125,834
hg38 chr16:2,075,833-2,075,833 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001077183.2:c.2580T>C NP_001070651.1:p.Phe860=
NM_001318827.1:c.2469T>C NP_001305756.1:p.Phe823=
NM_001318831.1:c.2469T>C NP_001305760.1:p.Phe823=
Summary

MGeND

Clinical significance Benign
Variant entry 1
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 191092 OMIM
HGNC 12363 HGNC
Ensembl ENSG00000103197 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv54381271 TogoVar
COSMIC COSM5019547 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign 2020/04/20 bronchus or lung, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-02-05 criteria provided, multiple submitters, no conflicts Tuberous sclerosis syndrome germline Detail
not provided no assertion provided Lymphangiomyomatosis germline Detail
Benign 2014-10-16 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2014-11-19 criteria provided, single submitter Hereditary cancer-predisposing syndrome germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts tuberous sclerosis 2 germline Detail
Benign 2023-11-30 criteria provided, multiple submitters, no conflicts not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 gastroesophageal reflux disease In subsequent logistic regression analyses, interactions between 2 SNPs (rs22957... BeFree 21751195 Detail
<0.001 Adenocarcinoma Of Esophagus In subsequent logistic regression analyses, interactions between 2 SNPs (rs22957... BeFree 21751195 Detail
<0.001 Adenocarcinoma Of Esophagus In subsequent logistic regression analyses, interactions between 2 SNPs (rs22957... BeFree 21751195 Detail
<0.001 Adenocarcinoma Of Esophagus In subsequent logistic regression analyses, interactions between 2 SNPs (rs22957... BeFree 21751195 Detail
<0.001 gastroesophageal reflux disease In subsequent logistic regression analyses, interactions between 2 SNPs (rs22957... BeFree 21751195 Detail
<0.001 gastroesophageal reflux disease In subsequent logistic regression analyses, interactions between 2 SNPs (rs22957... BeFree 21751195 Detail
<0.001 Adenocarcinoma Of Esophagus In subsequent logistic regression analyses, interactions between 2 SNPs (rs22957... BeFree 21751195 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000548.5(TSC2):c.2580T>C (p.Phe860=) AND Tuberous sclerosis syndrome ClinVar Detail
NM_000548.5(TSC2):c.2580T>C (p.Phe860=) AND Lymphangiomyomatosis ClinVar Detail
NM_000548.5(TSC2):c.2580T>C (p.Phe860=) AND not specified ClinVar Detail
NM_000548.5(TSC2):c.2580T>C (p.Phe860=) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000548.5(TSC2):c.2580T>C (p.Phe860=) AND Tuberous sclerosis 2 ClinVar Detail
NM_000548.5(TSC2):c.2580T>C (p.Phe860=) AND not provided ClinVar Detail
In subsequent logistic regression analyses, interactions between 2 SNPs (rs2295778 of HIF1AN, rs1333... DisGeNET Detail
In subsequent logistic regression analyses, interactions between 2 SNPs (rs2295778 of HIF1AN, rs1333... DisGeNET Detail
In subsequent logistic regression analyses, interactions between 2 SNPs (rs2295778 of HIF1AN, rs1333... DisGeNET Detail
In subsequent logistic regression analyses, interactions between 2 SNPs (rs2295778 of HIF1AN, rs1333... DisGeNET Detail
In subsequent logistic regression analyses, interactions between 2 SNPs (rs2295778 of HIF1AN, rs1333... DisGeNET Detail
In subsequent logistic regression analyses, interactions between 2 SNPs (rs2295778 of HIF1AN, rs1333... DisGeNET Detail
In subsequent logistic regression analyses, interactions between 2 SNPs (rs2295778 of HIF1AN, rs1333... 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
rs13337626 dbSNP
Genome
hg19
Position
chr16:2,125,834-2,125,834
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1189
Mean of sample read depth (HGVD)
37.33
Standard deviation of sample read depth (HGVD)
26.52
Number of reference allele (HGVD)
2377
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.2052144659377626E-4
Gene Symbol (HGVD)
TSC2
East Asian Chromosome Counts (ExAC)
8600
East Asian Allele Counts (ExAC)
13
East Asian Heterozygous Counts (ExAC)
13
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0015116279069767441
Chromosome Counts in All Race (ExAC)
119772
Allele Counts in All Race (ExAC)
8679
Heterozygous Counts in All Race (ExAC)
7899
Homozygous Counts in All Race (ExAC)
390
Allele Frequency in All Race (ExAC)
0.07246267909027151
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