Name: rs695871
Published: September 21, 2022
License: Open Access

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.

rs695871

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:111599196 (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: G>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.428207 (113342/264690, TOPMED)
G=0.391257 (53869/137682, GnomAD)
C=0.15328 (4294/28014, 14KJPN) (+ 15 more)
G=0.31462 (5935/18864, ALFA)
C=0.15453 (2563/16586, 8.3KJPN)
C=0.4433 (2839/6404, 1000G_30x)
C=0.4443 (2225/5008, 1000G)
G=0.2409 (1073/4454, Estonian)
C=0.1163 (285/2450, KOREAN)
C=0.1063 (186/1750, Korea1K)
G=0.202 (121/600, NorthernSweden)
G=0.257 (87/338, SGDP_PRJ)
C=0.381 (125/328, HapMap)
G=0.227 (49/216, GnomAD_exome)
G=0.472 (102/216, Qatari)
G=0.41 (14/34, GENOME_DK)
G=0.27 (7/26, Siberian)
G=0.1 (1/8, ExAC)

Clinical Significance: Reported in ClinVar
Gene : Consequence: ATXN2 : Non Coding Transcript Variant
ATXN2-AS : 2KB Upstream Variant
Publications: 5 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	18864	G=0.31462	C=0.68538
European	Sub	14260	G=0.22006	C=0.77994
African	Sub	2946	G=0.6884	C=0.3116
African Others	Sub	114	G=0.798	C=0.202
African American	Sub	2832	G=0.6840	C=0.3160
Asian	Sub	112	G=0.929	C=0.071
East Asian	Sub	86	G=0.93	C=0.07
Other Asian	Sub	26	G=0.92	C=0.08
Latin American 1	Sub	146	G=0.390	C=0.610
Latin American 2	Sub	610	G=0.495	C=0.505
South Asian	Sub	98	G=0.34	C=0.66
Other	Sub	692	G=0.395	C=0.605

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.428207	C=0.571793
gnomAD - Genomes	Global	Study-wide	137682	G=0.391257	C=0.608743
gnomAD - Genomes	European	Sub	74140	G=0.20970	C=0.79030
gnomAD - Genomes	African	Sub	41628	G=0.68646	C=0.31354
gnomAD - Genomes	American	Sub	13426	G=0.41948	C=0.58052
gnomAD - Genomes	Ashkenazi Jewish	Sub	3278	G=0.1290	C=0.8710
gnomAD - Genomes	East Asian	Sub	3098	G=0.9203	C=0.0797
gnomAD - Genomes	Other	Sub	2112	G=0.3977	C=0.6023
14KJPN	JAPANESE	Study-wide	28014	G=0.84672	C=0.15328
Allele Frequency Aggregator	Total	Global	18864	G=0.31462	C=0.68538
Allele Frequency Aggregator	European	Sub	14260	G=0.22006	C=0.77994
Allele Frequency Aggregator	African	Sub	2946	G=0.6884	C=0.3116
Allele Frequency Aggregator	Other	Sub	692	G=0.395	C=0.605
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.495	C=0.505
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.390	C=0.610
Allele Frequency Aggregator	Asian	Sub	112	G=0.929	C=0.071
Allele Frequency Aggregator	South Asian	Sub	98	G=0.34	C=0.66
8.3KJPN	JAPANESE	Study-wide	16586	G=0.84547	C=0.15453
1000Genomes_30x	Global	Study-wide	6404	G=0.5567	C=0.4433
1000Genomes_30x	African	Sub	1786	G=0.7844	C=0.2156
1000Genomes_30x	Europe	Sub	1266	G=0.2180	C=0.7820
1000Genomes_30x	South Asian	Sub	1202	G=0.3411	C=0.6589
1000Genomes_30x	East Asian	Sub	1170	G=0.8932	C=0.1068
1000Genomes_30x	American	Sub	980	G=0.442	C=0.558
1000Genomes	Global	Study-wide	5008	G=0.5557	C=0.4443
1000Genomes	African	Sub	1322	G=0.7821	C=0.2179
1000Genomes	East Asian	Sub	1008	G=0.8909	C=0.1091
1000Genomes	Europe	Sub	1006	G=0.2107	C=0.7893
1000Genomes	South Asian	Sub	978	G=0.334	C=0.666
1000Genomes	American	Sub	694	G=0.450	C=0.550
Genetic variation in the Estonian population	Estonian	Study-wide	4454	G=0.2409	C=0.7591
KOREAN population from KRGDB	KOREAN	Study-wide	2450	G=0.8837	C=0.1163
Korean Genome Project	KOREAN	Study-wide	1750	G=0.8937	C=0.1063
Northern Sweden	ACPOP	Study-wide	600	G=0.202	C=0.798
SGDP_PRJ	Global	Study-wide	338	G=0.257	A=0.003, C=0.740
HapMap	Global	Study-wide	328	G=0.619	C=0.381
HapMap	African	Sub	120	G=0.800	C=0.200
HapMap	American	Sub	120	G=0.275	C=0.725
HapMap	Asian	Sub	88	G=0.84	C=0.16
gnomAD - Exomes	Global	Study-wide	216	G=0.227	C=0.773
gnomAD - Exomes	European	Sub	210	G=0.219	C=0.781
gnomAD - Exomes	American	Sub	2	G=1.0	C=0.0
gnomAD - Exomes	Asian	Sub	2	G=0.5	C=0.5
gnomAD - Exomes	Other	Sub	2	G=0.0	C=1.0
gnomAD - Exomes	African	Sub	0	G=0	C=0
gnomAD - Exomes	Ashkenazi Jewish	Sub	0	G=0	C=0
Qatari	Global	Study-wide	216	G=0.472	C=0.528
The Danish reference pan genome	Danish	Study-wide	34	G=0.41	C=0.59
Siberian	Global	Study-wide	26	G=0.27	C=0.73
ExAC	Global	Study-wide	8	G=0.1	C=0.9
ExAC	Europe	Sub	6	G=0.0	C=1.0
ExAC	Asian	Sub	2	G=0.5	C=0.5
ExAC	African	Sub	0	G=0	C=0
ExAC	American	Sub	0	G=0	C=0
ExAC	Other	Sub	0	G=0	C=0

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 12	NC_000012.12:g.111599196G>A
GRCh38.p14 chr 12	NC_000012.12:g.111599196G>C
GRCh37.p13 chr 12	NC_000012.11:g.112037000G>A
GRCh37.p13 chr 12	NC_000012.11:g.112037000G>C
ATXN2 RefSeqGene (LRG_864)	NG_011572.3:g.5481C>T
ATXN2 RefSeqGene (LRG_864)	NG_011572.3:g.5481C>G

Gene: ATXN2, ataxin 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATXN2 transcript variant 2	NM_001310121.1:c.-65+379C… NM_001310121.1:c.-65+379C>T	N/A	Intron Variant
ATXN2 transcript variant 3	NM_001310123.1:c.-28+379C… NM_001310123.1:c.-28+379C>T	N/A	Intron Variant
ATXN2 transcript variant 1	NM_002973.4:c.-162=	N/A	5 Prime UTR Variant
ATXN2 transcript variant 5	NM_001372574.1:c.-162=	N/A	5 Prime UTR Variant
ATXN2 transcript variant 4	NR_132311.2:n.120C>T	N/A	Non Coding Transcript Variant
ATXN2 transcript variant 4	NR_132311.2:n.120C>G	N/A	Non Coding Transcript Variant

Gene: ATXN2-AS, ATXN2 antisense RNA (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
ATXN2-AS transcript	NR_146497.1:n.	N/A	Upstream Transcript Variant

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: C (allele ID: 133956 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000116477.8	not specified	Benign-Likely-Benign
RCV000625513.4	Spinocerebellar ataxia type 2	Benign

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	G=	A	C
GRCh38.p14 chr 12	NC_000012.12:g.111599196=	NC_000012.12:g.111599196G>A	NC_000012.12:g.111599196G>C
GRCh37.p13 chr 12	NC_000012.11:g.112037000=	NC_000012.11:g.112037000G>A	NC_000012.11:g.112037000G>C
ATXN2 RefSeqGene (LRG_864)	NG_011572.3:g.5481=	NG_011572.3:g.5481C>T	NG_011572.3:g.5481C>G
ATXN2 transcript variant 1	NM_002973.4:c.-162=	NM_002973.4:c.-162C>T	NM_002973.4:c.-162C>G
ATXN2 transcript variant 1	NM_002973.3:c.319=	NM_002973.3:c.319C>T	NM_002973.3:c.319C>G
ATXN2 transcript variant 4	NR_132311.2:n.120=	NR_132311.2:n.120C>T	NR_132311.2:n.120C>G
ATXN2 transcript variant 4	NR_132311.1:n.481=	NR_132311.1:n.481C>T	NR_132311.1:n.481C>G
ATXN2 transcript variant 5	NM_001372574.1:c.-162=	NM_001372574.1:c.-162C>T	NM_001372574.1:c.-162C>G
ATXN2 transcript variant 2	NM_001310121.1:c.-65+379=	NM_001310121.1:c.-65+379C>T	NM_001310121.1:c.-65+379C>G
ATXN2 transcript variant 3	NM_001310123.1:c.-28+379=	NM_001310123.1:c.-28+379C>T	NM_001310123.1:c.-28+379C>G
ataxin-2 isoform 1	NP_002964.3:p.Leu107=	NP_002964.3:p.Leu107Phe	NP_002964.3:p.Leu107Val

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#.

71 SubSNP, 18 Frequency, 2 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	FGU-CBT	ss869704	Aug 11, 2000 (83)
2	YUSUKE	ss3225938	Sep 28, 2001 (100)
3	MPIMG_RALS	ss23142228	Sep 20, 2004 (126)
4	BCMHGSC_JDW	ss89389421	Mar 24, 2008 (129)
5	HUMANGENOME_JCVI	ss97254366	Feb 06, 2009 (130)
6	ENSEMBL	ss133363762	Dec 01, 2009 (131)
7	ENSEMBL	ss144196525	Dec 01, 2009 (131)
8	ILLUMINA	ss160830223	Dec 01, 2009 (131)
9	BCM-HGSC-SUB	ss208415019	Jul 04, 2010 (132)
10	1000GENOMES	ss236090147	Jul 15, 2010 (132)
11	ILLUMINA	ss410800380	Sep 17, 2011 (135)
12	ILLUMINA	ss482420297	Sep 08, 2015 (146)
13	EXOME_CHIP	ss491473790	May 04, 2012 (137)
14	SSMP	ss658990542	Apr 25, 2013 (138)
15	EVA-GONL	ss989964082	Aug 21, 2014 (142)
16	1000GENOMES	ss1346656669	Aug 21, 2014 (142)
17	CLINVAR	ss1457613548	Nov 23, 2014 (142)
18	EVA_GENOME_DK	ss1576528126	Apr 01, 2015 (144)
19	EVA_EXAC	ss1691111628	Apr 01, 2015 (144)
20	WEILL_CORNELL_DGM	ss1933317403	Feb 12, 2016 (147)
21	JJLAB	ss2027415981	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2155765121	Dec 20, 2016 (150)
23	GRF	ss2700122801	Nov 08, 2017 (151)
24	GNOMAD	ss2740138386	Nov 08, 2017 (151)
25	GNOMAD	ss2748962050	Nov 08, 2017 (151)
26	GNOMAD	ss2915231195	Nov 08, 2017 (151)
27	SWEGEN	ss3010355666	Nov 08, 2017 (151)
28	CSHL	ss3350251578	Nov 08, 2017 (151)
29	ILLUMINA	ss3636209849	Oct 12, 2018 (152)
30	URBANLAB	ss3649923351	Oct 12, 2018 (152)
31	EGCUT_WGS	ss3677656104	Jul 13, 2019 (153)
32	EVA_DECODE	ss3694474965	Jul 13, 2019 (153)
33	ACPOP	ss3739386125	Jul 13, 2019 (153)
34	EVA	ss3750970728	Jul 13, 2019 (153)
35	PACBIO	ss3787337034	Jul 13, 2019 (153)
36	PACBIO	ss3792419254	Jul 13, 2019 (153)
37	PACBIO	ss3797302340	Jul 13, 2019 (153)
38	KHV_HUMAN_GENOMES	ss3816302923	Jul 13, 2019 (153)
39	EVA	ss3825829095	Apr 27, 2020 (154)
40	EVA	ss3833328479	Apr 27, 2020 (154)
41	EVA	ss3840236391	Apr 27, 2020 (154)
42	EVA	ss3845725027	Apr 27, 2020 (154)
43	SGDP_PRJ	ss3879121981	Apr 27, 2020 (154)
44	KRGDB	ss3927865004	Apr 27, 2020 (154)
45	KOGIC	ss3972736409	Apr 27, 2020 (154)
46	FSA-LAB	ss3984037605	Apr 26, 2021 (155)
47	EVA	ss3986586384	Apr 26, 2021 (155)
48	TOPMED	ss4932932765	Apr 26, 2021 (155)
49	TOMMO_GENOMICS	ss5208184686	Apr 26, 2021 (155)
50	EVA	ss5236909273	Apr 26, 2021 (155)
51	EVA	ss5237222021	Apr 26, 2021 (155)
52	1000G_HIGH_COVERAGE	ss5292249170	Oct 16, 2022 (156)
53	TRAN_CS_UWATERLOO	ss5314436723	Oct 16, 2022 (156)
54	EVA	ss5408256136	Oct 16, 2022 (156)
55	HUGCELL_USP	ss5486851225	Oct 16, 2022 (156)
56	EVA	ss5510845654	Oct 16, 2022 (156)
57	1000G_HIGH_COVERAGE	ss5590483332	Oct 16, 2022 (156)
58	EVA	ss5623959170	Oct 16, 2022 (156)
59	EVA	ss5624036747	Oct 16, 2022 (156)
60	SANFORD_IMAGENETICS	ss5653965595	Oct 16, 2022 (156)
61	TOMMO_GENOMICS	ss5758514189	Oct 16, 2022 (156)
62	EVA	ss5799448922	Oct 16, 2022 (156)
63	EVA	ss5800065636	Oct 16, 2022 (156)
64	EVA	ss5800180393	Oct 16, 2022 (156)
65	YY_MCH	ss5813649245	Oct 16, 2022 (156)
66	EVA	ss5838520411	Oct 16, 2022 (156)
67	EVA	ss5848363119	Oct 16, 2022 (156)
68	EVA	ss5906040318	Oct 16, 2022 (156)
69	EVA	ss5936554513	Oct 16, 2022 (156)
70	EVA	ss5945372863	Oct 16, 2022 (156)
71	EVA	ss5980761540	Oct 16, 2022 (156)
72	1000Genomes	NC_000012.11 - 112037000	Oct 12, 2018 (152)
73	1000Genomes_30x	NC_000012.12 - 111599196	Oct 16, 2022 (156)
74	Genetic variation in the Estonian population	NC_000012.11 - 112037000	Oct 12, 2018 (152)
75	ExAC	NC_000012.11 - 112037000	Oct 12, 2018 (152)
76	The Danish reference pan genome	NC_000012.11 - 112037000	Apr 27, 2020 (154)
77	gnomAD - Genomes	NC_000012.12 - 111599196	Apr 26, 2021 (155)
78	gnomAD - Exomes	NC_000012.11 - 112037000	Jul 13, 2019 (153)
79	HapMap	NC_000012.12 - 111599196	Apr 27, 2020 (154)
80	KOREAN population from KRGDB	NC_000012.11 - 112037000	Apr 27, 2020 (154)
81	Korean Genome Project	NC_000012.12 - 111599196	Apr 27, 2020 (154)
82	Northern Sweden	NC_000012.11 - 112037000	Jul 13, 2019 (153)
83	Qatari	NC_000012.11 - 112037000	Apr 27, 2020 (154)
84	SGDP_PRJ	NC_000012.11 - 112037000	Apr 27, 2020 (154)
85	Siberian	NC_000012.11 - 112037000	Apr 27, 2020 (154)
86	8.3KJPN	NC_000012.11 - 112037000	Apr 26, 2021 (155)
87	14KJPN	NC_000012.12 - 111599196	Oct 16, 2022 (156)
88	TopMed	NC_000012.12 - 111599196	Apr 26, 2021 (155)
89	ALFA	NC_000012.12 - 111599196	Apr 26, 2021 (155)
90	ClinVar	RCV000116477.8	Oct 16, 2022 (156)
91	ClinVar	RCV000625513.4	Oct 16, 2022 (156)

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)
rs17235360	Mar 11, 2006 (126)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
31138961, ss3879121981	NC_000012.11:112036999:G:A	NC_000012.12:111599195:G:A	(self)
ss89389421, ss160830223, ss208415019	NC_000012.10:110521382:G:C	NC_000012.12:111599195:G:C	(self)
59468104, 23394352, 1426269, 3129194, 9376707, 35042398, 12670990, 15359333, 31138961, 8281475, 66153993, ss236090147, ss482420297, ss491473790, ss658990542, ss989964082, ss1346656669, ss1576528126, ss1691111628, ss1933317403, ss2027415981, ss2155765121, ss2700122801, ss2740138386, ss2748962050, ss2915231195, ss3010355666, ss3350251578, ss3636209849, ss3677656104, ss3739386125, ss3750970728, ss3787337034, ss3792419254, ss3797302340, ss3825829095, ss3833328479, ss3840236391, ss3879121981, ss3927865004, ss3984037605, ss3986586384, ss5208184686, ss5408256136, ss5510845654, ss5623959170, ss5624036747, ss5653965595, ss5799448922, ss5800065636, ss5800180393, ss5838520411, ss5848363119, ss5936554513, ss5945372863, ss5980761540	NC_000012.11:112036999:G:C	NC_000012.12:111599195:G:C	(self)
RCV000116477.8, RCV000625513.4, 78009267, 419470532, 905511, 29114410, 92351293, 148478422, 7715206232, ss1457613548, ss3649923351, ss3694474965, ss3816302923, ss3845725027, ss3972736409, ss4932932765, ss5236909273, ss5237222021, ss5292249170, ss5314436723, ss5486851225, ss5590483332, ss5758514189, ss5813649245, ss5906040318	NC_000012.12:111599195:G:C	NC_000012.12:111599195:G:C	(self)
ss869704, ss3225938, ss23142228, ss97254366, ss133363762, ss144196525, ss410800380	NT_009775.17:2613529:G:C	NC_000012.12:111599195:G:C	(self)

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

5 citations for rs695871

PMID	Title	Author	Year	Journal
16205789	Positive selection of a pre-expansion CAG repeat of the human SCA2 gene.	Yu F et al.	2005	PLoS genetics
20016785	Genetic variance in the spinocerebellar ataxia type 2 (ATXN2) gene in children with severe early onset obesity.	Figueroa KP et al.	2009	PloS one
22916186	ATXN2 and its neighbouring gene SH2B3 are associated with increased ALS risk in the Turkish population.	Lahut S et al.	2012	PloS one
33058338	A Novel Duplication in ATXN2 as Modifier for Spinocerebellar Ataxia 3 (SCA3) and C9ORF72-ALS.	Laffita-Mesa JM et al.	2021	Movement disorders
34298214	SCA2 in the Indian population: Unified haplotype and variable phenotypic patterns in a large case series.	Sonakar AK et al.	2021	Parkinsonism & related disorders

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs695871