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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

All alleles are reported in the Forward orientation. Click on the Variant Details tab for details on Genomic Placement, Gene, and Amino Acid changes. HGVS names are in the HGVS tab.

Reference SNP (rs) Report

This page reports data for a single dbSNP Reference SNP variation (RefSNP or rs) from the new redesigned dbSNP build.
Top of the page reports a concise summary for the rs, with more specific details included in the corresponding tabs below.
All alleles are reported in the Forward orientation. Use the Genomic View to inspect the nucleotides flanking the variant, and its neighbors.
For more information see Help documentation.

rs587779817

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr11:108251026-108251030 (GRCh38.p13) Help

The anchor position for this RefSNP. Includes all nucleotides potentially affected by this change, thus it can differ from HGVS, which is right-shifted. See here for details.

Alleles
delGA
Variation Type
Indel Insertion and Deletion
Frequency
delGA=0.000049 (13/264690, TOPMED)
delGA=0.000056 (14/250850, GnomAD_exome)
delGA=0.000057 (8/140204, GnomAD) (+ 4 more)
delGA=0.000050 (6/120956, ExAC)
delGA=0.00000 (0/78636, PAGE_STUDY)
delGA=0.00000 (0/14050, ALFA)
delGA=0.00024 (3/12512, GO-ESP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ATM : Frameshift Variant
Publications
6 citations
Genomic View
See rs on genome
Help

Variant Details tab shows known variant placements on genomic sequences: chromosomes (NC_), RefSeqGene, pseudogenes or genomic regions (NG_), and in a separate table: on transcripts (NM_) and protein sequences (NP_). The corresponding transcript and protein locations are listed in adjacent lines, along with molecular consequences from Sequence Ontology. When no protein placement is available, only the transcript is listed. Column "Codon[Amino acid]" shows the actual base change in the format of "Reference > Alternate" allele, including the nucleotide codon change in transcripts, and the amino acid change in proteins, respectively, allowing for known ribosomal slippage sites. To view nucleotides adjacent to the variant use the Genomic View at the bottom of the page - zoom into the sequence until the nucleotides around the variant become visible.

Genomic Placements
Sequence name Change
GRCh38.p13 chr 11 NC_000011.10:g.108251027GA[1]
GRCh37.p13 chr 11 NC_000011.9:g.108121754GA[1]
ATM RefSeqGene (LRG_135) NG_009830.1:g.33196GA[1]
Gene: ATM, ATM serine/threonine kinase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ATM transcript variant 3 NM_001351835.2:c. N/A Genic Downstream Transcript Variant
ATM transcript variant 4 NM_001351836.2:c. N/A Genic Downstream Transcript Variant
ATM transcript variant 1 NM_001351834.2:c.1564_156…

NM_001351834.2:c.1564_1565del

E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform a NP_001338763.1:p.Glu522fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant 2 NM_000051.4:c.1564_1565del E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform a NP_000042.3:p.Glu522fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant X12 XM_006718845.2:c. N/A Genic Upstream Transcript Variant
ATM transcript variant X7 XM_011542843.2:c.1564_156…

XM_011542843.2:c.1564_1565del

E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform X3 XP_011541145.1:p.Glu522fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant X10 XM_017017791.1:c.1564_156…

XM_017017791.1:c.1564_1565del

E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform X6 XP_016873280.1:p.Glu522fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant X1 XM_011542840.3:c.1564_156…

XM_011542840.3:c.1564_1565del

E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform X1 XP_011541142.1:p.Glu522fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant X2 XM_006718843.4:c.1564_156…

XM_006718843.4:c.1564_1565del

E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform X1 XP_006718906.1:p.Glu522fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant X3 XM_017017789.2:c.1564_156…

XM_017017789.2:c.1564_1565del

E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform X1 XP_016873278.1:p.Glu522fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant X4 XM_005271562.5:c.1564_156…

XM_005271562.5:c.1564_1565del

E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform X1 XP_005271619.2:p.Glu522fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant X5 XM_017017790.2:c.1564_156…

XM_017017790.2:c.1564_1565del

E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform X1 XP_016873279.1:p.Glu522fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant X6 XM_011542842.3:c.1399_140…

XM_011542842.3:c.1399_1400del

E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform X2 XP_011541144.1:p.Glu467fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant X8 XM_011542844.3:c.520_521d…

XM_011542844.3:c.520_521del

E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform X4 XP_011541146.1:p.Glu174fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant X9 XM_011542845.2:c.256_257d…

XM_011542845.2:c.256_257del

E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform X5 XP_011541147.1:p.Glu86fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant X11 XM_017017792.2:c.1564_156…

XM_017017792.2:c.1564_1565del

E [GA] > I [A] Coding Sequence Variant
serine-protein kinase ATM isoform X7 XP_016873281.1:p.Glu522fs E (Glu) > I (Ile) Frameshift Variant
ATM transcript variant X13 XR_002957150.1:n.2295GA[1] N/A Non Coding Transcript Variant
Help

Clinical Significance tab shows a list of clinical significance entries from ClinVar associated with the variation, per allele. Click on the RCV accession (i.e. RCV000001615.2) or Allele ID (i.e. 12274) to access full ClinVar report.

Allele: delGA (allele ID: 132797 )
ClinVar Accession Disease Names Clinical Significance
RCV000115144.12 Hereditary cancer-predisposing syndrome Pathogenic
RCV000169147.13 Ataxia-telangiectasia syndrome Pathogenic
RCV000211964.7 not provided Pathogenic
RCV000709705.4 Familial cancer of breast Pathogenic
RCV001263302.1 Seizures Pathogenic

ALFA Allele Frequency
The ALFA project provide aggregate allele frequency from dbGaP. More information is available on the project page including descriptions, data access, and terms of use.

Release Version: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 14050 AGAGA=1.00000 AGA=0.00000
European Sub 9690 AGAGA=1.0000 AGA=0.0000
African Sub 2898 AGAGA=1.0000 AGA=0.0000
African Others Sub 114 AGAGA=1.000 AGA=0.000
African American Sub 2784 AGAGA=1.0000 AGA=0.0000
Asian Sub 112 AGAGA=1.000 AGA=0.000
East Asian Sub 86 AGAGA=1.00 AGA=0.00
Other Asian Sub 26 AGAGA=1.00 AGA=0.00
Latin American 1 Sub 146 AGAGA=1.000 AGA=0.000
Latin American 2 Sub 610 AGAGA=1.000 AGA=0.000
South Asian Sub 98 AGAGA=1.00 AGA=0.00
Other Sub 496 AGAGA=1.000 AGA=0.000


Help

Frequency tab displays a table of the reference and alternate allele frequencies reported by various studies and populations. Table lines, where Population="Global" refer to the entire study population, whereas lines, where Group="Sub", refer to a study-specific population subgroupings (i.e. AFR, CAU, etc.), if available. Frequency for the alternate allele (Alt Allele) is a ratio of samples observed-to-total, where the numerator (observed samples) is the number of chromosomes in the study with the minor allele present (found in "Sample size", where Group="Sub"), and the denominator (total samples) is the total number of all chromosomes in the study for the variant (found in "Sample size", where Group="Study-wide" and Population="Global").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 AGAGA=0.999951 delGA=0.000049
gnomAD - Exomes Global Study-wide 250850 AGAGA=0.999944 delGA=0.000056
gnomAD - Exomes European Sub 135166 AGAGA=0.999911 delGA=0.000089
gnomAD - Exomes Asian Sub 49004 AGAGA=1.00000 delGA=0.00000
gnomAD - Exomes American Sub 34584 AGAGA=1.00000 delGA=0.00000
gnomAD - Exomes African Sub 15924 AGAGA=1.00000 delGA=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10074 AGAGA=1.00000 delGA=0.00000
gnomAD - Exomes Other Sub 6098 AGAGA=0.9997 delGA=0.0003
gnomAD - Genomes Global Study-wide 140204 AGAGA=0.999943 delGA=0.000057
gnomAD - Genomes European Sub 75932 AGAGA=0.99989 delGA=0.00011
gnomAD - Genomes African Sub 42024 AGAGA=1.00000 delGA=0.00000
gnomAD - Genomes American Sub 13640 AGAGA=1.00000 delGA=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 AGAGA=1.0000 delGA=0.0000
gnomAD - Genomes East Asian Sub 3130 AGAGA=1.0000 delGA=0.0000
gnomAD - Genomes Other Sub 2154 AGAGA=1.0000 delGA=0.0000
ExAC Global Study-wide 120956 AGAGA=0.999950 delGA=0.000050
ExAC Europe Sub 73312 AGAGA=0.99992 delGA=0.00008
ExAC Asian Sub 25154 AGAGA=1.00000 delGA=0.00000
ExAC American Sub 11562 AGAGA=1.00000 delGA=0.00000
ExAC African Sub 10020 AGAGA=1.00000 delGA=0.00000
ExAC Other Sub 908 AGAGA=1.000 delGA=0.000
The PAGE Study Global Study-wide 78636 AGAGA=1.00000 delGA=0.00000
The PAGE Study AfricanAmerican Sub 32486 AGAGA=1.00000 delGA=0.00000
The PAGE Study Mexican Sub 10796 AGAGA=1.00000 delGA=0.00000
The PAGE Study Asian Sub 8314 AGAGA=1.0000 delGA=0.0000
The PAGE Study PuertoRican Sub 7912 AGAGA=1.0000 delGA=0.0000
The PAGE Study NativeHawaiian Sub 4532 AGAGA=1.0000 delGA=0.0000
The PAGE Study Cuban Sub 4228 AGAGA=1.0000 delGA=0.0000
The PAGE Study Dominican Sub 3824 AGAGA=1.0000 delGA=0.0000
The PAGE Study CentralAmerican Sub 2448 AGAGA=1.0000 delGA=0.0000
The PAGE Study SouthAmerican Sub 1982 AGAGA=1.0000 delGA=0.0000
The PAGE Study NativeAmerican Sub 1258 AGAGA=1.0000 delGA=0.0000
The PAGE Study SouthAsian Sub 856 AGAGA=1.000 delGA=0.000
GO Exome Sequencing Project Global Study-wide 12512 AGAGA=0.99976 delGA=0.00024
GO Exome Sequencing Project European American Sub 8250 AGAGA=0.9999 delGA=0.0001
GO Exome Sequencing Project African American Sub 4262 AGAGA=0.9995 delGA=0.0005
Help

Aliases tab displays HGVS names representing the variant placements and allele changes on genomic, transcript and protein sequences, per allele. HGVS name is an expression for reporting sequence accession and version, sequence type, position, and allele change. The column "Note" can have two values: "diff" means that there is a difference between the reference allele (variation interval) at the placement reported in HGVS name and the reference alleles reported in other HGVS names, and "rev" means that the sequence of this variation interval at the placement reported in HGVS name is in reverse orientation to the sequence(s) of this variation in other HGVS names not labeled as "rev".

Placement AGAGA= delGA
GRCh38.p13 chr 11 NC_000011.10:g.108251026_108251030= NC_000011.10:g.108251027GA[1]
GRCh37.p13 chr 11 NC_000011.9:g.108121753_108121757= NC_000011.9:g.108121754GA[1]
ATM RefSeqGene (LRG_135) NG_009830.1:g.33195_33199= NG_009830.1:g.33196GA[1]
ATM transcript variant 2 NM_000051.4:c.1561_1565= NM_000051.4:c.1564_1565del
ATM transcript variant 2 NM_000051.3:c.1561_1565= NM_000051.3:c.1564_1565del
ATM transcript variant 1 NM_001351834.2:c.1561_1565= NM_001351834.2:c.1564_1565del
ATM transcript variant 1 NM_001351834.1:c.1561_1565= NM_001351834.1:c.1564_1565del
ATM transcript variant X4 XM_005271562.5:c.1561_1565= XM_005271562.5:c.1564_1565del
ATM transcript variant X2 XM_005271562.1:c.1561_1565= XM_005271562.1:c.1564_1565del
ATM transcript variant X2 XM_006718843.4:c.1561_1565= XM_006718843.4:c.1564_1565del
ATM transcript variant X8 XM_011542844.3:c.517_521= XM_011542844.3:c.520_521del
ATM transcript variant X1 XM_011542840.3:c.1561_1565= XM_011542840.3:c.1564_1565del
ATM transcript variant X6 XM_011542842.3:c.1396_1400= XM_011542842.3:c.1399_1400del
ATM transcript variant X3 XM_017017789.2:c.1561_1565= XM_017017789.2:c.1564_1565del
ATM transcript variant X5 XM_017017790.2:c.1561_1565= XM_017017790.2:c.1564_1565del
ATM transcript variant X7 XM_011542843.2:c.1561_1565= XM_011542843.2:c.1564_1565del
ATM transcript variant X9 XM_011542845.2:c.253_257= XM_011542845.2:c.256_257del
ATM transcript variant X11 XM_017017792.2:c.1561_1565= XM_017017792.2:c.1564_1565del
ATM transcript variant X10 XM_017017791.1:c.1561_1565= XM_017017791.1:c.1564_1565del
ATM transcript variant X13 XR_002957150.1:n.2294_2298= XR_002957150.1:n.2295GA[1]
serine-protein kinase ATM isoform a NP_000042.3:p.Arg521_Glu522= NP_000042.3:p.Glu522fs
serine-protein kinase ATM isoform a NP_001338763.1:p.Arg521_Glu522= NP_001338763.1:p.Glu522fs
serine-protein kinase ATM isoform X1 XP_005271619.2:p.Arg521_Glu522= XP_005271619.2:p.Glu522fs
serine-protein kinase ATM isoform X1 XP_006718906.1:p.Arg521_Glu522= XP_006718906.1:p.Glu522fs
serine-protein kinase ATM isoform X4 XP_011541146.1:p.Arg173_Glu174= XP_011541146.1:p.Glu174fs
serine-protein kinase ATM isoform X1 XP_011541142.1:p.Arg521_Glu522= XP_011541142.1:p.Glu522fs
serine-protein kinase ATM isoform X2 XP_011541144.1:p.Arg466_Glu467= XP_011541144.1:p.Glu467fs
serine-protein kinase ATM isoform X1 XP_016873278.1:p.Arg521_Glu522= XP_016873278.1:p.Glu522fs
serine-protein kinase ATM isoform X1 XP_016873279.1:p.Arg521_Glu522= XP_016873279.1:p.Glu522fs
serine-protein kinase ATM isoform X3 XP_011541145.1:p.Arg521_Glu522= XP_011541145.1:p.Glu522fs
serine-protein kinase ATM isoform X5 XP_011541147.1:p.Arg85_Glu86= XP_011541147.1:p.Glu86fs
serine-protein kinase ATM isoform X7 XP_016873281.1:p.Arg521_Glu522= XP_016873281.1:p.Glu522fs
serine-protein kinase ATM isoform X6 XP_016873280.1:p.Arg521_Glu522= XP_016873280.1:p.Glu522fs
serine-protein kinase ATM isoform X2 XP_005271619.1:p.Arg521_Glu522= XP_005271619.1:p.Glu522fs
Help

Submissions tab displays variations originally submitted to dbSNP, now supporting this RefSNP cluster (rs). We display Submitter handle, Submission identifier, Date and Build number, when the submission appeared for the first time. Direct submissions to dbSNP have Submission ID in the form of an ss-prefixed number (ss#). Other supporting variations are listed in the table without ss#.

19 SubSNP, 7 Frequency, 5 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss1457612481 Nov 23, 2014 (142)
2 EVA_EXAC ss1711988019 Apr 01, 2015 (136)
3 CLINVAR ss1751113414 May 21, 2015 (136)
4 ILLUMINA ss1946321982 Feb 12, 2016 (136)
5 ILLUMINA ss1959383685 Feb 12, 2016 (136)
6 GNOMAD ss2739369800 Nov 08, 2017 (151)
7 AFFY ss2984955801 Nov 08, 2017 (151)
8 ILLUMINA ss3021373995 Nov 08, 2017 (151)
9 TOPMED ss3155836667 Nov 08, 2017 (151)
10 ILLUMINA ss3625609146 Oct 12, 2018 (152)
11 ILLUMINA ss3644574837 Oct 12, 2018 (152)
12 ILLUMINA ss3651741135 Oct 12, 2018 (152)
13 ILLUMINA ss3653728528 Oct 12, 2018 (152)
14 ILLUMINA ss3725274455 Jul 13, 2019 (153)
15 ILLUMINA ss3744090397 Jul 13, 2019 (153)
16 PAGE_CC ss3771651046 Jul 13, 2019 (153)
17 EVA ss3824668904 Apr 26, 2020 (154)
18 GNOMAD ss4242133817 Apr 27, 2021 (155)
19 TOPMED ss4899217145 Apr 27, 2021 (155)
20 ExAC NC_000011.9 - 108121753 Oct 12, 2018 (152)
21 gnomAD - Genomes NC_000011.10 - 108251026 Apr 27, 2021 (155)
22 gnomAD - Exomes NC_000011.9 - 108121753 Jul 13, 2019 (153)
23 GO Exome Sequencing Project NC_000011.9 - 108121753 Oct 12, 2018 (152)
24 The PAGE Study NC_000011.10 - 108251026 Jul 13, 2019 (153)
25 TopMed NC_000011.10 - 108251026 Apr 27, 2021 (155)
26 ALFA NC_000011.10 - 108251026 Apr 27, 2021 (155)
27 ClinVar RCV000115144.12 Apr 27, 2021 (155)
28 ClinVar RCV000169147.13 Apr 27, 2021 (155)
29 ClinVar RCV000211964.7 Apr 27, 2021 (155)
30 ClinVar RCV000709705.4 Apr 27, 2021 (155)
31 ClinVar RCV001263302.1 Apr 27, 2021 (155)
Help

History tab displays RefSNPs (Associated ID) from previous builds (Build) that now support the current RefSNP, and the dates, when the history was updated for each Associated ID (History Updated).

Associated ID History Updated (Build)
rs751357509 May 11, 2017 (136)
rs786204256 Jun 25, 2015 (136)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
895990, 8587676, 1126444, ss1711988019, ss1946321982, ss1959383685, ss2739369800, ss2984955801, ss3021373995, ss3625609146, ss3644574837, ss3651741135, ss3653728528, ss3744090397, ss3824668904 NC_000011.9:108121752:AG: NC_000011.10:108251025:AGAGA:AGA (self)
391346057, 872515, 71957168, 114762801, ss1751113414, ss3155836667, ss3725274455, ss3771651046, ss4242133817, ss4899217145 NC_000011.10:108251025:AG: NC_000011.10:108251025:AGAGA:AGA (self)
RCV000115144.12, RCV000169147.13, RCV000211964.7, RCV000709705.4, RCV001263302.1, 6633327983 NC_000011.10:108251025:AGAGA:AGA NC_000011.10:108251025:AGAGA:AGA (self)
ss1457612481 NC_000011.10:108251028:GA: NC_000011.10:108251025:AGAGA:AGA (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

6 citations for rs587779817
PMID Title Author Year Journal
8789452 Mutations revealed by sequencing the 5' half of the gene for ataxia telangiectasia. Byrd PJ et al. 1996 Human molecular genetics
10330348 Splicing defects in the ataxia-telangiectasia gene, ATM: underlying mutations and consequences. Teraoka SN et al. 1999 American journal of human genetics
10817650 Mutations at the ataxia-telangiectasia locus and clinical phenotypes of A-T patients. Li A et al. 2000 American journal of medical genetics
16266405 ATM gene founder haplotypes and associated mutations in Polish families with ataxia-telangiectasia. Mitui M et al. 2005 Annals of human genetics
21965147 New mutations in the ATM gene and clinical data of 25 AT patients. Demuth I et al. 2011 Neurogenetics
22213089 Presence of ATM protein and residual kinase activity correlates with the phenotype in ataxia-telangiectasia: a genotype-phenotype study. Verhagen MM et al. 2012 Human mutation
Help

The Flanks tab provides retrieving flanking sequences of a SNP on all molecules that have placements.

Genome context:
Select flank length:

Genomic regions, transcripts, and products
Top Help

NCBI Graphical Sequence Viewer display of the genomic region, transcripts and protein products for the reported RefSNP (rs).
Use the zoom option to view the nucleotides around the RefSNP and find other neighboring RefSNPs.
Visit Sequence Viewer for help with navigating inside the display and modifying the selection of displayed data tracks.

Software version is: 2.0.1.post596+ae089ad