chr17:42564502:A>G Detail (hg38) (COASY)

Information

Genome

Assembly Position
hg19 chr17:40,716,520-40,716,520 View the variant detail on this assembly version.
hg38 chr17:42,564,502-42,564,502

HGVS

Type Transcript Protein
RefSeq NM_025233.6:c.972A>G NP_079509.5:p.Thr324=
NM_001042529.2:c.972A>G NP_001035994.1:p.Thr324=
NM_001042532.3:c.1059A>G NP_001035997.2:p.Thr353=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.453
ToMMo:0.461
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.439

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 609855 OMIM
HGNC 29932 HGNC
Ensembl ENSG00000068120 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv57817262 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2015-12-02 criteria provided, single submitter not specified germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts neurodegeneration with brain iron accumulation 6 germline Detail
Benign 2021-07-22 criteria provided, single submitter Pontocerebellar hypoplasia, type 12 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.101 Malignant neoplasm of breast However, when this relation was assessed within strata based on estrogen-related... BeFree 22199302 Detail
0.240 Malignant neoplasm of breast However, when this relation was assessed within strata based on estrogen-related... BeFree 22199302 Detail
0.028 Malignant neoplasm of breast However, when this relation was assessed within strata based on estrogen-related... BeFree 22199302 Detail
0.005 Mammographic Density However, when this relation was assessed within strata based on estrogen-related... BeFree 22199302 Detail
0.003 Mammographic Density However, when this relation was assessed within strata based on estrogen-related... BeFree 22199302 Detail
0.080 breast carcinoma However, when this relation was assessed within strata based on estrogen-related... BeFree 22199302 Detail
0.004 breast carcinoma However, when this relation was assessed within strata based on estrogen-related... BeFree 22199302 Detail
0.003 Mammographic Density However, when this relation was assessed within strata based on estrogen-related... BeFree 22199302 Detail
0.021 breast carcinoma However, when this relation was assessed within strata based on estrogen-related... BeFree 22199302 Detail
0.004 breast carcinoma However, when this relation was assessed within strata based on estrogen-related... BeFree 22199302 Detail
0.006 Mammographic Density However, when this relation was assessed within strata based on estrogen-related... BeFree 22199302 Detail
0.042 Malignant neoplasm of breast However, when this relation was assessed within strata based on estrogen-related... BeFree 22199302 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_025233.7(COASY):c.972A>G (p.Thr324=) AND not specified ClinVar Detail
NM_025233.7(COASY):c.972A>G (p.Thr324=) AND Neurodegeneration with brain iron accumulation 6 ClinVar Detail
NM_025233.7(COASY):c.972A>G (p.Thr324=) AND Pontocerebellar hypoplasia, type 12 ClinVar Detail
However, when this relation was assessed within strata based on estrogen-related factors, a few SNPs... DisGeNET Detail
However, when this relation was assessed within strata based on estrogen-related factors, a few SNPs... DisGeNET Detail
However, when this relation was assessed within strata based on estrogen-related factors, a few SNPs... DisGeNET Detail
However, when this relation was assessed within strata based on estrogen-related factors, a few SNPs... DisGeNET Detail
However, when this relation was assessed within strata based on estrogen-related factors, a few SNPs... DisGeNET Detail
However, when this relation was assessed within strata based on estrogen-related factors, a few SNPs... DisGeNET Detail
However, when this relation was assessed within strata based on estrogen-related factors, a few SNPs... DisGeNET Detail
However, when this relation was assessed within strata based on estrogen-related factors, a few SNPs... DisGeNET Detail
However, when this relation was assessed within strata based on estrogen-related factors, a few SNPs... DisGeNET Detail
However, when this relation was assessed within strata based on estrogen-related factors, a few SNPs... DisGeNET Detail
However, when this relation was assessed within strata based on estrogen-related factors, a few SNPs... DisGeNET Detail
However, when this relation was assessed within strata based on estrogen-related factors, a few SNPs... 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
rs598126 dbSNP
Genome
hg38
Position
chr17:42,564,502-42,564,502
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
168.56
Standard deviation of sample read depth (HGVD)
79.46
Number of reference allele (HGVD)
1323
Number of alternative allele (HGVD)
1097
Allele Frequency (HGVD)
0.45330578512396696
Gene Symbol (HGVD)
COASY
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))
rs598126
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4605
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7718
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8630
East Asian Allele Counts (ExAC)
3792
East Asian Heterozygous Counts (ExAC)
2228
East Asian Homozygous Counts (ExAC)
782
East Asian Allele Frequency (ExAC)
0.43939745075318654
Chromosome Counts in All Race (ExAC)
121304
Allele Counts in All Race (ExAC)
65032
Heterozygous Counts in All Race (ExAC)
29468
Homozygous Counts in All Race (ExAC)
17782
Allele Frequency in All Race (ExAC)
0.5361076304161445
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