chr2:17780821:T>C Detail (hg38) (SMC6, GEN1)

Information

Genome

Assembly Position
hg19 chr2:17,962,088-17,962,088 View the variant detail on this assembly version.
hg38 chr2:17,780,821-17,780,821

HGVS

Type Transcript Protein
RefSeq NM_182625.4:c.1609T>C NP_872431.4:p.Cys537Arg
NM_001130009.2:c.1609T>C NP_001123481.2:p.Cys537Arg
Ensemble ENST00000317402.11:c.1609T>C ENST00000317402.11:p.Cys537Arg
Type Transcript Protein
RefSeq
Ensemble ENST00000402989.5:c.-6+6994A>G
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 Uncertain significance
Review star
Show details
Links
Type Database ID Link
Gene MIM 612449 OMIM
HGNC 26881 HGNC
Ensembl ENSG00000178295 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6008256 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 609387 OMIM
HGNC 20466 HGNC
Ensembl ENSG00000163029 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv6008256 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Uncertain significance 2023-09-06 criteria provided, single submitter not provided germline Detail
Uncertain significance 2022-02-17 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
[No Data.]
Annotation

Annotations

DescrptionSourceLinks
NM_001130009.3(GEN1):c.1609T>C (p.Cys537Arg) AND not provided ClinVar Detail
NM_001130009.3(GEN1):c.1609T>C (p.Cys537Arg) AND not specified 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
rs765356309 dbSNP
Genome
hg38
Position
chr2:17,780,821-17,780,821
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
98.55
Standard deviation of sample read depth (HGVD)
47.08
Number of reference allele (HGVD)
2419
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1322314049586776E-4
Gene Symbol (HGVD)
GEN1
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))
rs765356309
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0004
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
6
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)
2
East Asian Heterozygous Counts (ExAC)
2
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
2.3137436372049977E-4
Chromosome Counts in All Race (ExAC)
121214
Allele Counts in All Race (ExAC)
3
Heterozygous Counts in All Race (ExAC)
3
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
2.4749616380946097E-5
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