chr11:108304735:G>A Detail (hg38) (ATM)

Information

Genome

Assembly Position
hg19 chr11:108,175,462-108,175,462 View the variant detail on this assembly version.
hg38 chr11:108,304,735-108,304,735

HGVS

Type Transcript Protein
RefSeq NM_000051.3:c.5557G>A NP_000042.3:p.Asp1853Asn
NM_001351834.1:c.5557G>A NP_001338763.1:p.Asp1853Asn
Ensemble ENST00000278616.10:c.5557G>A ENST00000278616.10:p.Asp1853Asn
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:0.007

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 607585 OMIM
HGNC 795 HGNC
Ensembl ENSG00000149311 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv43963658 TogoVar
COSMIC COSM41596 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, multiple submitters, no conflicts not specified germline Detail
Benign 2021-05-03 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts Ataxia-telangiectasia syndrome germline unknown Detail
Benign 2023-11-30 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2022-04-19 criteria provided, single submitter hereditary breast ovarian cancer syndrome germline Detail
Benign 2023-07-07 criteria provided, single submitter Familial cancer of breast germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.002 Papillary thyroid carcinoma In the analyses of ATM/TP53 (rs1801516/rs664677/rs609429/rs1042522) combinations... BeFree 19286843 Detail
0.246 melanoma Finally, rs1801516, located on the ATM gene, showed a trend towards a protective... BeFree 23537197 Detail
0.002 Carcinoma of bladder We examined the associations between bladder cancer and 7 polymorphisms from 5 g... BeFree 22927776 Detail
0.047 breast carcinoma Single nucleotide polymorphism D1853N of the ATM gene may alter the risk for bre... BeFree 18264724 Detail
<0.001 Malignant neoplasm of pancreas The homozygous mutant genotype of LIG3 G-39A [odds ratio (OR), 0.23; 95% confide... BeFree 19147782 Detail
0.002 pancreatic carcinoma A statistically significant interaction of ATM D1853N and LIG4 C54T genotype wit... BeFree 19147782 Detail
0.047 breast carcinoma The association between ATM D1853N polymorphism and breast cancer susceptibility... BeFree 20799949 Detail
0.002 cervix carcinoma Genetic polymorphisms and cervical cancer development: ATM G5557A and p53bp1 C12... BeFree 22200742 Detail
0.128 Malignant neoplasm of breast The association between ATM D1853N polymorphism and breast cancer susceptibility... BeFree 20799949 Detail
0.006 Carcinoma of bladder We examined the associations between bladder cancer and 7 polymorphisms from 5 g... BeFree 22927776 Detail
<0.001 diabetes mellitus A statistically significant interaction of ATM D1853N and LIG4 C54T genotype wit... BeFree 19147782 Detail
0.002 Carcinoma of bladder We examined the associations between bladder cancer and 7 polymorphisms from 5 g... BeFree 22927776 Detail
0.002 Malignant tumor of cervix Genetic polymorphisms and cervical cancer development: ATM G5557A and p53bp1 C12... BeFree 22200742 Detail
<0.001 Paroxysmal atrial tachycardia We examined the associations between bladder cancer and 7 polymorphisms from 5 g... BeFree 22927776 Detail
<0.001 Astrocytoma Three-hit hypothesis in astrocytoma: tracing the polymorphism D1853N in ATM gene... BeFree 18465141 Detail
0.128 Malignant neoplasm of breast Importance of ATM gene as a susceptible trait: predisposition role of D1853N pol... BeFree 20396981 Detail
<0.001 pancreatic carcinoma The homozygous mutant genotype of LIG3 G-39A [odds ratio (OR), 0.23; 95% confide... BeFree 19147782 Detail
<0.001 pancreatic carcinoma A statistically significant interaction of ATM D1853N and LIG4 C54T genotype wit... BeFree 19147782 Detail
<0.001 Diabetes A statistically significant interaction of ATM D1853N and LIG4 C54T genotype wit... BeFree 19147782 Detail
0.047 breast carcinoma Importance of ATM gene as a susceptible trait: predisposition role of D1853N pol... BeFree 20396981 Detail
<0.001 pancreatic carcinoma The homozygous mutant genotype of LIG3 G-39A [odds ratio (OR), 0.23; 95% confide... BeFree 19147782 Detail
<0.001 cervix carcinoma Genetic polymorphisms and cervical cancer development: ATM G5557A and p53bp1 C12... BeFree 22200742 Detail
<0.001 Paroxysmal atrial tachycardia We examined the associations between bladder cancer and 7 polymorphisms from 5 g... BeFree 22927776 Detail
0.128 Malignant neoplasm of breast Single nucleotide polymorphism D1853N of the ATM gene may alter the risk for bre... BeFree 18264724 Detail
<0.001 diabetes mellitus A statistically significant interaction of ATM D1853N and LIG4 C54T genotype wit... BeFree 19147782 Detail
<0.001 Diabetes A statistically significant interaction of ATM D1853N and LIG4 C54T genotype wit... BeFree 19147782 Detail
0.001 bilateral breast cancer The common ATM polymorphism 5557G&gt;A (p.D1853N) (rs1801516), previously sugges... BeFree 18264724 Detail
0.012 Malignant neoplasm of urinary bladder We examined the associations between bladder cancer and 7 polymorphisms from 5 g... BeFree 22927776 Detail
<0.001 Malignant neoplasm of pancreas A statistically significant interaction of ATM D1853N and LIG4 C54T genotype wit... BeFree 19147782 Detail
<0.001 Papillary thyroid carcinoma The ATM G5557A and XRCC1 Arg399Gln polymorphisms, regardless of radiation exposu... BeFree 19286843 Detail
<0.001 Malignant tumor of cervix Genetic polymorphisms and cervical cancer development: ATM G5557A and p53bp1 C12... BeFree 22200742 Detail
0.002 cervix carcinoma Analysis of D1853N ATM polymorphism in radiosensitive patients with cervical car... BeFree 22250480 Detail
<0.001 Brain Tumor, Primary Three-hit hypothesis in astrocytoma: tracing the polymorphism D1853N in ATM gene... BeFree 18465141 Detail
0.004 Malignant neoplasm of pancreas A statistically significant interaction of ATM D1853N and LIG4 C54T genotype wit... BeFree 19147782 Detail
0.002 Malignant neoplasm of urinary bladder We examined the associations between bladder cancer and 7 polymorphisms from 5 g... BeFree 22927776 Detail
0.001 bilateral breast cancer Recently, a common ATM variant, ATMivs38 -8T&gt;C in cis with the ATMex39 5557G&... BeFree 16914028 Detail
0.032 Malignant neoplasm of urinary bladder We examined the associations between bladder cancer and 7 polymorphisms from 5 g... BeFree 22927776 Detail
0.006 Brain Neoplasms The involvement of ATM gene and specifically, the important role of D1853N polym... BeFree 20396981 Detail
0.128 Malignant neoplasm of breast The results of this study suggest an association between the ATM codon 1853 Asn/... BeFree 16338099 Detail
<0.001 Malignant neoplasm of pancreas The homozygous mutant genotype of LIG3 G-39A [odds ratio (OR), 0.23; 95% confide... BeFree 19147782 Detail
0.006 Paroxysmal atrial tachycardia We examined the associations between bladder cancer and 7 polymorphisms from 5 g... BeFree 22927776 Detail
0.047 breast carcinoma The results of this study suggest an association between the ATM codon 1853 Asn/... BeFree 16338099 Detail
0.246 melanoma Genome-wide association study identifies three new melanoma susceptibility loci. GWASCAT 21983787 Detail
0.246 melanoma [Genome-wide association study identifies three new melanoma susceptibility loci... GAD 21983787 Detail
0.006 Papillary thyroid carcinoma In the analyses of ATM/TP53 (rs1801516/rs664677/rs609429/rs1042522) combinations... BeFree 19286843 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000051.4(ATM):c.5557G>A (p.Asp1853Asn) AND not specified ClinVar Detail
NM_000051.4(ATM):c.5557G>A (p.Asp1853Asn) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000051.4(ATM):c.5557G>A (p.Asp1853Asn) AND Ataxia-telangiectasia syndrome ClinVar Detail
NM_000051.4(ATM):c.5557G>A (p.Asp1853Asn) AND not provided ClinVar Detail
NM_000051.4(ATM):c.5557G>A (p.Asp1853Asn) AND Hereditary breast ovarian cancer syndrome ClinVar Detail
NM_000051.4(ATM):c.5557G>A (p.Asp1853Asn) AND Familial cancer of breast ClinVar Detail
In the analyses of ATM/TP53 (rs1801516/rs664677/rs609429/rs1042522) combinations, the GG/TC/CG/GC ge... DisGeNET Detail
Finally, rs1801516, located on the ATM gene, showed a trend towards a protective role in MM similar ... DisGeNET Detail
We examined the associations between bladder cancer and 7 polymorphisms from 5 genes involved in the... DisGeNET Detail
Single nucleotide polymorphism D1853N of the ATM gene may alter the risk for breast cancer. DisGeNET Detail
The homozygous mutant genotype of LIG3 G-39A [odds ratio (OR), 0.23; 95% confidence interval (CI), 0... DisGeNET Detail
A statistically significant interaction of ATM D1853N and LIG4 C54T genotype with diabetes on the ri... DisGeNET Detail
The association between ATM D1853N polymorphism and breast cancer susceptibility: a meta-analysis. DisGeNET Detail
Genetic polymorphisms and cervical cancer development: ATM G5557A and p53bp1 C1236G. DisGeNET Detail
The association between ATM D1853N polymorphism and breast cancer susceptibility: a meta-analysis. DisGeNET Detail
We examined the associations between bladder cancer and 7 polymorphisms from 5 genes involved in the... DisGeNET Detail
A statistically significant interaction of ATM D1853N and LIG4 C54T genotype with diabetes on the ri... DisGeNET Detail
We examined the associations between bladder cancer and 7 polymorphisms from 5 genes involved in the... DisGeNET Detail
Genetic polymorphisms and cervical cancer development: ATM G5557A and p53bp1 C1236G. DisGeNET Detail
We examined the associations between bladder cancer and 7 polymorphisms from 5 genes involved in the... DisGeNET Detail
Three-hit hypothesis in astrocytoma: tracing the polymorphism D1853N in ATM gene through a pedigree ... DisGeNET Detail
Importance of ATM gene as a susceptible trait: predisposition role of D1853N polymorphism in breast ... DisGeNET Detail
The homozygous mutant genotype of LIG3 G-39A [odds ratio (OR), 0.23; 95% confidence interval (CI), 0... DisGeNET Detail
A statistically significant interaction of ATM D1853N and LIG4 C54T genotype with diabetes on the ri... DisGeNET Detail
A statistically significant interaction of ATM D1853N and LIG4 C54T genotype with diabetes on the ri... DisGeNET Detail
Importance of ATM gene as a susceptible trait: predisposition role of D1853N polymorphism in breast ... DisGeNET Detail
The homozygous mutant genotype of LIG3 G-39A [odds ratio (OR), 0.23; 95% confidence interval (CI), 0... DisGeNET Detail
Genetic polymorphisms and cervical cancer development: ATM G5557A and p53bp1 C1236G. DisGeNET Detail
We examined the associations between bladder cancer and 7 polymorphisms from 5 genes involved in the... DisGeNET Detail
Single nucleotide polymorphism D1853N of the ATM gene may alter the risk for breast cancer. DisGeNET Detail
A statistically significant interaction of ATM D1853N and LIG4 C54T genotype with diabetes on the ri... DisGeNET Detail
A statistically significant interaction of ATM D1853N and LIG4 C54T genotype with diabetes on the ri... DisGeNET Detail
The common ATM polymorphism 5557G&gt;A (p.D1853N) (rs1801516), previously suggested to be associated... DisGeNET Detail
We examined the associations between bladder cancer and 7 polymorphisms from 5 genes involved in the... DisGeNET Detail
A statistically significant interaction of ATM D1853N and LIG4 C54T genotype with diabetes on the ri... DisGeNET Detail
The ATM G5557A and XRCC1 Arg399Gln polymorphisms, regardless of radiation exposure, associated with ... DisGeNET Detail
Genetic polymorphisms and cervical cancer development: ATM G5557A and p53bp1 C1236G. DisGeNET Detail
Analysis of D1853N ATM polymorphism in radiosensitive patients with cervical carcinoma. DisGeNET Detail
Three-hit hypothesis in astrocytoma: tracing the polymorphism D1853N in ATM gene through a pedigree ... DisGeNET Detail
A statistically significant interaction of ATM D1853N and LIG4 C54T genotype with diabetes on the ri... DisGeNET Detail
We examined the associations between bladder cancer and 7 polymorphisms from 5 genes involved in the... DisGeNET Detail
Recently, a common ATM variant, ATMivs38 -8T&gt;C in cis with the ATMex39 5557G&gt;A (D1853N) varian... DisGeNET Detail
We examined the associations between bladder cancer and 7 polymorphisms from 5 genes involved in the... DisGeNET Detail
The involvement of ATM gene and specifically, the important role of D1853N polymorphism, as a three-... DisGeNET Detail
The results of this study suggest an association between the ATM codon 1853 Asn/Asp and Asn/Asn geno... DisGeNET Detail
The homozygous mutant genotype of LIG3 G-39A [odds ratio (OR), 0.23; 95% confidence interval (CI), 0... DisGeNET Detail
We examined the associations between bladder cancer and 7 polymorphisms from 5 genes involved in the... DisGeNET Detail
The results of this study suggest an association between the ATM codon 1853 Asn/Asp and Asn/Asn geno... DisGeNET Detail
Genome-wide association study identifies three new melanoma susceptibility loci. DisGeNET Detail
[Genome-wide association study identifies three new melanoma susceptibility loci.] DisGeNET Detail
In the analyses of ATM/TP53 (rs1801516/rs664677/rs609429/rs1042522) combinations, the GG/TC/CG/GC ge... 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
rs1801516 dbSNP
Genome
hg38
Position
chr11:108,304,735-108,304,735
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
71.50
Standard deviation of sample read depth (HGVD)
33.39
Number of reference allele (HGVD)
2419
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1322314049586776E-4
Gene Symbol (HGVD)
ATM
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))
rs1801516
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))
16758
East Asian Chromosome Counts (ExAC)
8594
East Asian Allele Counts (ExAC)
57
East Asian Heterozygous Counts (ExAC)
57
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.006632534326274145
Chromosome Counts in All Race (ExAC)
120820
Allele Counts in All Race (ExAC)
13307
Heterozygous Counts in All Race (ExAC)
11401
Homozygous Counts in All Race (ExAC)
953
Allele Frequency in All Race (ExAC)
0.11013904982618772
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