chr16:2085339:G>A Detail (hg38) (TSC2)

Information

Genome

Assembly Position
hg19 chr16:2,135,340-2,135,340 View the variant detail on this assembly version.
hg38 chr16:2,085,339-2,085,339

HGVS

Type Transcript Protein
RefSeq NM_000548.4:c.4662+17G>A
NM_001114382.2:c.4593+17G>A
NM_001318829.1:c.4317+17G>A
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:<0.001

Prediction

ClinVar

Clinical Significance Benign Likely 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 tgv54383332 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
not provided no assertion provided Tuberous sclerosis syndrome germline Detail
Likely benign 2017-04-06 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign Likely benign 2024-01-17 criteria provided, multiple submitters, no conflicts tuberous sclerosis 2 germline Detail
Likely benign 2021-12-14 criteria provided, single submitter Isolated focal cortical dysplasia type II,Lymphangiomyomatosis,tuberous sclerosis 2 unknown Detail
Likely benign 2021-12-14 criteria provided, single submitter Isolated focal cortical dysplasia type II,Lymphangiomyomatosis,tuberous sclerosis 2 unknown Detail
Likely benign 2021-12-14 criteria provided, single submitter Isolated focal cortical dysplasia type II,Lymphangiomyomatosis,tuberous sclerosis 2 unknown Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_000548.5(TSC2):c.4662+17G>A AND Tuberous sclerosis syndrome ClinVar Detail
NM_000548.5(TSC2):c.4662+17G>A AND not specified ClinVar Detail
NM_000548.5(TSC2):c.4662+17G>A AND Tuberous sclerosis 2 ClinVar Detail
NM_000548.5(TSC2):c.4662+17G>A AND multiple conditions ClinVar Detail
NM_000548.5(TSC2):c.4662+17G>A AND multiple conditions ClinVar Detail
NM_000548.5(TSC2):c.4662+17G>A AND multiple conditions ClinVar Detail

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs45443002 dbSNP
Genome
hg38
Position
chr16:2,085,339-2,085,339
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
833
Mean of sample read depth (HGVD)
169.97
Standard deviation of sample read depth (HGVD)
81.24
Number of reference allele (HGVD)
1665
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
6.002400960384153E-4
Gene Symbol (HGVD)
TSC2
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))
rs45443002
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0005
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8564
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
118778
Allele Counts in All Race (ExAC)
9
Heterozygous Counts in All Race (ExAC)
9
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
7.577160753674922E-5
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