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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.

rs569392621

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr14:92071015 (GRCh38.p14) 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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000009 (1/113460, ExAC)
C=0.00000 (0/11862, ALFA)
C=0.0004 (2/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ATXN3 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 11862 T=1.00000 C=0.00000
European Sub 7618 T=1.0000 C=0.0000
African Sub 2816 T=1.0000 C=0.0000
African Others Sub 108 T=1.000 C=0.000
African American Sub 2708 T=1.0000 C=0.0000
Asian Sub 108 T=1.000 C=0.000
East Asian Sub 84 T=1.00 C=0.00
Other Asian Sub 24 T=1.00 C=0.00
Latin American 1 Sub 146 T=1.000 C=0.000
Latin American 2 Sub 610 T=1.000 C=0.000
South Asian Sub 94 T=1.00 C=0.00
Other Sub 470 T=1.000 C=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
ExAC Global Study-wide 113460 T=0.999991 C=0.000009
ExAC Europe Sub 69384 T=1.00000 C=0.00000
ExAC Asian Sub 23334 T=1.00000 C=0.00000
ExAC American Sub 11096 T=1.00000 C=0.00000
ExAC African Sub 8792 T=0.9999 C=0.0001
ExAC Other Sub 854 T=1.000 C=0.000
Allele Frequency Aggregator Total Global 11862 T=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 7618 T=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 2816 T=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 T=1.000 C=0.000
Allele Frequency Aggregator Other Sub 470 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 108 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 94 T=1.00 C=0.00
1000Genomes Global Study-wide 5008 T=0.9996 C=0.0004
1000Genomes African Sub 1322 T=0.9985 C=0.0015
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=1.000 C=0.000
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.p14 chr 14 NC_000014.9:g.92071015T>C
GRCh37.p13 chr 14 NC_000014.8:g.92537359T>C
ATXN3 RefSeqGene (LRG_865) NG_008198.2:g.40607A>G
LOC108663987 genomic region NG_051545.1:g.105T>C
Gene: ATXN3, ataxin 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ATXN3 transcript variant reference NM_004993.6:c.911A>G Q [CAG] > R [CGG] Coding Sequence Variant
ataxin-3 reference isoform NP_004984.2:p.Gln304Arg Q (Gln) > R (Arg) Missense Variant
ATXN3 transcript variant o NM_001164778.2:c.426A>G A [GCA] > A [GCG] Coding Sequence Variant
ataxin-3 isoform o NP_001158250.1:p.Ala142= A (Ala) > A (Ala) Synonymous Variant
ATXN3 transcript variant u NM_001164780.2:c.374A>G Q [CAG] > R [CGG] Coding Sequence Variant
ataxin-3 isoform u NP_001158252.1:p.Gln125Arg Q (Gln) > R (Arg) Missense Variant
ATXN3 transcript variant j NM_001164777.2:c.108A>G A [GCA] > A [GCG] Coding Sequence Variant
ataxin-3 isoform j NP_001158249.1:p.Ala36= A (Ala) > A (Ala) Synonymous Variant
ATXN3 transcript variant ae NM_001164782.2:c.63A>G A [GCA] > A [GCG] Coding Sequence Variant
ataxin-3 isoform ae NP_001158254.1:p.Ala21= A (Ala) > A (Ala) Synonymous Variant
ATXN3 transcript variant b NM_001164774.2:c.228A>G A [GCA] > A [GCG] Coding Sequence Variant
ataxin-3 isoform b NP_001158246.1:p.Ala76= A (Ala) > A (Ala) Synonymous Variant
ATXN3 transcript variant r NM_001164779.2:c.548A>G Q [CAG] > R [CGG] Coding Sequence Variant
ataxin-3 isoform r NP_001158251.1:p.Gln183Arg Q (Gln) > R (Arg) Missense Variant
ATXN3 transcript variant g NM_001164776.2:c.273A>G A [GCA] > A [GCG] Coding Sequence Variant
ataxin-3 isoform g NP_001158248.1:p.Ala91= A (Ala) > A (Ala) Synonymous Variant
ATXN3 transcript variant h NM_030660.5:c.746A>G Q [CAG] > R [CGG] Coding Sequence Variant
ataxin-3 isoform h NP_109376.1:p.Gln249Arg Q (Gln) > R (Arg) Missense Variant
ATXN3 transcript variant ad NM_001127696.2:c.866A>G Q [CAG] > R [CGG] Coding Sequence Variant
ataxin-3 isoform ad NP_001121168.1:p.Gln289Arg Q (Gln) > R (Arg) Missense Variant
ATXN3 transcript variant e NM_001127697.3:c.758A>G Q [CAG] > R [CGG] Coding Sequence Variant
ataxin-3 isoform e NP_001121169.2:p.Gln253Arg Q (Gln) > R (Arg) Missense Variant
ATXN3 transcript variant y NM_001164781.2:c.701A>G Q [CAG] > R [CGG] Coding Sequence Variant
ataxin-3 isoform y NP_001158253.1:p.Gln234Arg Q (Gln) > R (Arg) Missense Variant
ATXN3 transcript variant n NR_028460.2:n.370A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant v NR_028464.2:n.842A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant z NR_028467.2:n.856A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant t NR_028463.2:n.544A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant af NR_028469.2:n.702A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant k NR_028457.2:n.1000A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant l NR_028458.2:n.844A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant p NR_028461.2:n.853A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant f NR_028455.2:n.909A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant q NR_028462.2:n.832A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant a NR_028453.2:n.855A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant c NR_031765.2:n.357A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant am NR_028470.2:n.160A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant m NR_028459.2:n.995A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant w NR_028465.2:n.864A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant x NR_028466.2:n.490A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant i NR_028456.2:n.744A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant ac NR_028468.2:n.688A>G N/A Non Coding Transcript Variant
ATXN3 transcript variant d NR_028454.2:n.690A>G 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.

Not Reported in ClinVar
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 T= C
GRCh38.p14 chr 14 NC_000014.9:g.92071015= NC_000014.9:g.92071015T>C
GRCh37.p13 chr 14 NC_000014.8:g.92537359= NC_000014.8:g.92537359T>C
ATXN3 RefSeqGene (LRG_865) NG_008198.2:g.40607= NG_008198.2:g.40607A>G
ATXN3 transcript variant reference NM_004993.6:c.911= NM_004993.6:c.911A>G
ATXN3 transcript variant reference NM_004993.5:c.911= NM_004993.5:c.911A>G
ATXN3 transcript variant h NM_030660.5:c.746= NM_030660.5:c.746A>G
ATXN3 transcript variant h NM_030660.4:c.746= NM_030660.4:c.746A>G
ATXN3 transcript variant e NM_001127697.3:c.758= NM_001127697.3:c.758A>G
ATXN3 transcript variant e NM_001127697.2:c.758= NM_001127697.2:c.758A>G
ATXN3 transcript variant k NR_028457.2:n.1000= NR_028457.2:n.1000A>G
ATXN3 transcript variant k NR_028457.1:n.1039= NR_028457.1:n.1039A>G
ATXN3 transcript variant m NR_028459.2:n.995= NR_028459.2:n.995A>G
ATXN3 transcript variant m NR_028459.1:n.1034= NR_028459.1:n.1034A>G
ATXN3 transcript variant f NR_028455.2:n.909= NR_028455.2:n.909A>G
ATXN3 transcript variant f NR_028455.1:n.948= NR_028455.1:n.948A>G
ATXN3 transcript variant ad NM_001127696.2:c.866= NM_001127696.2:c.866A>G
ATXN3 transcript variant ad NM_001127696.1:c.866= NM_001127696.1:c.866A>G
ATXN3 transcript variant w NR_028465.2:n.864= NR_028465.2:n.864A>G
ATXN3 transcript variant w NR_028465.1:n.903= NR_028465.1:n.903A>G
ATXN3 transcript variant z NR_028467.2:n.856= NR_028467.2:n.856A>G
ATXN3 transcript variant z NR_028467.1:n.895= NR_028467.1:n.895A>G
ATXN3 transcript variant a NR_028453.2:n.855= NR_028453.2:n.855A>G
ATXN3 transcript variant a NR_028453.1:n.894= NR_028453.1:n.894A>G
ATXN3 transcript variant p NR_028461.2:n.853= NR_028461.2:n.853A>G
ATXN3 transcript variant p NR_028461.1:n.892= NR_028461.1:n.892A>G
ATXN3 transcript variant l NR_028458.2:n.844= NR_028458.2:n.844A>G
ATXN3 transcript variant l NR_028458.1:n.883= NR_028458.1:n.883A>G
ATXN3 transcript variant v NR_028464.2:n.842= NR_028464.2:n.842A>G
ATXN3 transcript variant v NR_028464.1:n.881= NR_028464.1:n.881A>G
ATXN3 transcript variant q NR_028462.2:n.832= NR_028462.2:n.832A>G
ATXN3 transcript variant q NR_028462.1:n.871= NR_028462.1:n.871A>G
ATXN3 transcript variant i NR_028456.2:n.744= NR_028456.2:n.744A>G
ATXN3 transcript variant i NR_028456.1:n.783= NR_028456.1:n.783A>G
ATXN3 transcript variant y NM_001164781.2:c.701= NM_001164781.2:c.701A>G
ATXN3 transcript variant y NM_001164781.1:c.701= NM_001164781.1:c.701A>G
ATXN3 transcript variant af NR_028469.2:n.702= NR_028469.2:n.702A>G
ATXN3 transcript variant af NR_028469.1:n.741= NR_028469.1:n.741A>G
ATXN3 transcript variant d NR_028454.2:n.690= NR_028454.2:n.690A>G
ATXN3 transcript variant d NR_028454.1:n.729= NR_028454.1:n.729A>G
ATXN3 transcript variant ac NR_028468.2:n.688= NR_028468.2:n.688A>G
ATXN3 transcript variant ac NR_028468.1:n.727= NR_028468.1:n.727A>G
ATXN3 transcript variant u NM_001164780.2:c.374= NM_001164780.2:c.374A>G
ATXN3 transcript variant u NM_001164780.1:c.374= NM_001164780.1:c.374A>G
ATXN3 transcript variant r NM_001164779.2:c.548= NM_001164779.2:c.548A>G
ATXN3 transcript variant r NM_001164779.1:c.548= NM_001164779.1:c.548A>G
ATXN3 transcript variant t NR_028463.2:n.544= NR_028463.2:n.544A>G
ATXN3 transcript variant t NR_028463.1:n.583= NR_028463.1:n.583A>G
ATXN3 transcript variant x NR_028466.2:n.490= NR_028466.2:n.490A>G
ATXN3 transcript variant x NR_028466.1:n.529= NR_028466.1:n.529A>G
ATXN3 transcript variant o NM_001164778.2:c.426= NM_001164778.2:c.426A>G
ATXN3 transcript variant o NM_001164778.1:c.426= NM_001164778.1:c.426A>G
ATXN3 transcript variant n NR_028460.2:n.370= NR_028460.2:n.370A>G
ATXN3 transcript variant n NR_028460.1:n.409= NR_028460.1:n.409A>G
ATXN3 transcript variant c NR_031765.2:n.357= NR_031765.2:n.357A>G
ATXN3 transcript variant c NR_031765.1:n.396= NR_031765.1:n.396A>G
ATXN3 transcript variant g NM_001164776.2:c.273= NM_001164776.2:c.273A>G
ATXN3 transcript variant g NM_001164776.1:c.273= NM_001164776.1:c.273A>G
ATXN3 transcript variant b NM_001164774.2:c.228= NM_001164774.2:c.228A>G
ATXN3 transcript variant b NM_001164774.1:c.228= NM_001164774.1:c.228A>G
ATXN3 transcript variant am NR_028470.2:n.160= NR_028470.2:n.160A>G
ATXN3 transcript variant am NR_028470.1:n.199= NR_028470.1:n.199A>G
ATXN3 transcript variant j NM_001164777.2:c.108= NM_001164777.2:c.108A>G
ATXN3 transcript variant j NM_001164777.1:c.108= NM_001164777.1:c.108A>G
ATXN3 transcript variant ae NM_001164782.2:c.63= NM_001164782.2:c.63A>G
ATXN3 transcript variant ae NM_001164782.1:c.63= NM_001164782.1:c.63A>G
LOC108663987 genomic region NG_051545.1:g.105= NG_051545.1:g.105T>C
ATXN3 transcript variant c NM_001164775.1:c.188= NM_001164775.1:c.188A>G
ATXN3 transcript variant 3 NM_001024631.1:c.*585= NM_001024631.1:c.*585A>G
ataxin-3 reference isoform NP_004984.2:p.Gln304= NP_004984.2:p.Gln304Arg
ataxin-3 isoform h NP_109376.1:p.Gln249= NP_109376.1:p.Gln249Arg
ataxin-3 isoform e NP_001121169.2:p.Gln253= NP_001121169.2:p.Gln253Arg
ataxin-3 isoform ad NP_001121168.1:p.Gln289= NP_001121168.1:p.Gln289Arg
ataxin-3 isoform y NP_001158253.1:p.Gln234= NP_001158253.1:p.Gln234Arg
ataxin-3 isoform u NP_001158252.1:p.Gln125= NP_001158252.1:p.Gln125Arg
ataxin-3 isoform r NP_001158251.1:p.Gln183= NP_001158251.1:p.Gln183Arg
ataxin-3 isoform o NP_001158250.1:p.Ala142= NP_001158250.1:p.Ala142=
ataxin-3 isoform g NP_001158248.1:p.Ala91= NP_001158248.1:p.Ala91=
ataxin-3 isoform b NP_001158246.1:p.Ala76= NP_001158246.1:p.Ala76=
ataxin-3 isoform j NP_001158249.1:p.Ala36= NP_001158249.1:p.Ala36=
ataxin-3 isoform ae NP_001158254.1:p.Ala21= NP_001158254.1:p.Ala21=
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#.

4 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1352139307 Aug 21, 2014 (142)
2 EVA_EXAC ss1691599977 Apr 01, 2015 (144)
3 EVA ss5417078597 Oct 16, 2022 (156)
4 EVA ss5902489352 Oct 16, 2022 (156)
5 1000Genomes NC_000014.8 - 92537359 Oct 12, 2018 (152)
6 ExAC NC_000014.8 - 92537359 Oct 12, 2018 (152)
7 ALFA NC_000014.9 - 92071015 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
65163296, 1955050, ss1352139307, ss1691599977, ss5417078597 NC_000014.8:92537358:T:C NC_000014.9:92071014:T:C (self)
13881503583, ss5902489352 NC_000014.9:92071014:T:C NC_000014.9:92071014:T:C (self)
Help

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

No publications for rs569392621

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.post761+d5e8e07