chr2:201289477:C>T Detail (hg38) (CASP8, FLACC1)

Information

Genome

Assembly Position
hg19 chr2:202,154,200-202,154,200 View the variant detail on this assembly version.
hg38 chr2:201,289,477-201,289,477

HGVS

Type Transcript Protein
RefSeq
Ensemble ENST00000696069.1:c.1259+4160C>T
Type Transcript Protein
RefSeq NM_001127391.2:c.1122G>A NP_001120863.1:p.Thr374=
NM_139163.3:c.1191G>A NP_631902.2:p.Thr397=
NM_001289993.1:c.1122G>A NP_001276922.1:p.Thr374=
Summary

MGeND

Clinical significance
Variant entry
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:<0.001

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601763 OMIM
HGNC 1509 HGNC
Ensembl ENSG00000064012 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv10142887 TogoVar
COSMIC
MONDO
Type Database ID Link
Gene MIM 619796 OMIM
HGNC 14439 HGNC
Ensembl ENSG00000155749 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv10142887 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2016-03-28 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.162 Malignant neoplasm of breast Consistent with their breast cancer associations, rs3817198 (LSP1) and rs1328161... BeFree 20145138 Detail
0.004 breast carcinoma Consistent with their breast cancer associations, rs3817198 (LSP1) and rs1328161... BeFree 20145138 Detail
0.049 Malignant neoplasm of breast Consistent with their breast cancer associations, rs3817198 (LSP1) and rs1328161... BeFree 20145138 Detail
0.166 Malignant neoplasm of breast Consistent with their breast cancer associations, rs3817198 (LSP1) and rs1328161... BeFree 20145138 Detail
0.006 breast carcinoma Consistent with their breast cancer associations, rs3817198 (LSP1) and rs1328161... BeFree 20145138 Detail
0.009 breast carcinoma Consistent with their breast cancer associations, rs3817198 (LSP1) and rs1328161... BeFree 20145138 Detail
0.006 breast carcinoma Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.009 breast carcinoma Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.031 breast carcinoma Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.001 Malignant neoplasm of breast Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.162 Malignant neoplasm of breast Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.002 breast carcinoma Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.001 breast carcinoma Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.004 breast carcinoma Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.131 Malignant neoplasm of breast Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.049 Malignant neoplasm of breast Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.166 Malignant neoplasm of breast Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.090 Malignant neoplasm of breast Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.019 breast carcinoma Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
0.230 Malignant neoplasm of breast Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2),... BeFree 22532573 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001127391.3(FLACC1):c.1122G>A (p.Thr374=) AND not specified ClinVar Detail
Consistent with their breast cancer associations, rs3817198 (LSP1) and rs13281615 (8q) were associat... DisGeNET Detail
Consistent with their breast cancer associations, rs3817198 (LSP1) and rs13281615 (8q) were associat... DisGeNET Detail
Consistent with their breast cancer associations, rs3817198 (LSP1) and rs13281615 (8q) were associat... DisGeNET Detail
Consistent with their breast cancer associations, rs3817198 (LSP1) and rs13281615 (8q) were associat... DisGeNET Detail
Consistent with their breast cancer associations, rs3817198 (LSP1) and rs13281615 (8q) were associat... DisGeNET Detail
Consistent with their breast cancer associations, rs3817198 (LSP1) and rs13281615 (8q) were associat... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... DisGeNET Detail
Confirmed BC risk SNPs rs17468277 (CASP8), rs1982073 (TGFB1), rs2981582 (FGFR2), rs13281615 (8q24), ... 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
rs17468277 dbSNP
Genome
hg38
Position
chr2:201,289,477-201,289,477
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
158.94
Standard deviation of sample read depth (HGVD)
71.62
Number of reference allele (HGVD)
2417
Number of alternative allele (HGVD)
3
Allele Frequency (HGVD)
0.0012396694214876034
Gene Symbol (HGVD)
ALS2CR12
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
3
East Asian Heterozygous Counts (ExAC)
3
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
3.4666050381326557E-4
Chromosome Counts in All Race (ExAC)
121356
Allele Counts in All Race (ExAC)
10972
Heterozygous Counts in All Race (ExAC)
9694
Homozygous Counts in All Race (ExAC)
639
Allele Frequency in All Race (ExAC)
0.09041168133425624
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