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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.

rs34835885

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:32100345 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.246160 (65156/264690, TOPMED)
A=0.247073 (32750/132552, GnomAD)
A=0.33691 (9445/28034, 14KJPN) (+ 16 more)
A=0.19483 (5015/25740, ALFA)
A=0.33725 (5595/16590, 8.3KJPN)
A=0.2922 (1871/6404, 1000G_30x)
A=0.2971 (1488/5008, 1000G)
A=0.2634 (1144/4344, Estonian)
A=0.2828 (1090/3854, ALSPAC)
A=0.2702 (1002/3708, TWINSUK)
A=0.4044 (1185/2930, KOREAN)
A=0.4017 (736/1832, Korea1K)
A=0.301 (300/998, GoNL)
A=0.183 (103/562, NorthernSweden)
G=0.345 (87/252, SGDP_PRJ)
A=0.245 (53/216, Qatari)
A=0.12 (5/40, GENOME_DK)
G=0.50 (15/30, Siberian)
A=0.50 (15/30, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SPAST : Intron 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 25740 G=0.80466 A=0.19483, T=0.00051, C=0.00000
European Sub 21210 G=0.78260 A=0.21678, T=0.00061, C=0.00000
African Sub 2298 G=0.9795 A=0.0205, T=0.0000, C=0.0000
African Others Sub 98 G=0.97 A=0.03, T=0.00, C=0.00
African American Sub 2200 G=0.9800 A=0.0200, T=0.0000, C=0.0000
Asian Sub 48 G=0.81 A=0.19, T=0.00, C=0.00
East Asian Sub 38 G=0.82 A=0.18, T=0.00, C=0.00
Other Asian Sub 10 G=0.8 A=0.2, T=0.0, C=0.0
Latin American 1 Sub 112 G=0.946 A=0.054, T=0.000, C=0.000
Latin American 2 Sub 392 G=0.952 A=0.048, T=0.000, C=0.000
South Asian Sub 54 G=0.83 A=0.17, T=0.00, C=0.00
Other Sub 1626 G=0.7989 A=0.2011, T=0.0000, C=0.0000


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 G=0.753840 A=0.246160
gnomAD - Genomes Global Study-wide 132552 G=0.752927 A=0.247073
gnomAD - Genomes European Sub 71758 G=0.72728 A=0.27272
gnomAD - Genomes African Sub 39620 G=0.82163 A=0.17837
gnomAD - Genomes American Sub 12810 G=0.73872 A=0.26128
gnomAD - Genomes Ashkenazi Jewish Sub 3276 G=0.7640 A=0.2360
gnomAD - Genomes East Asian Sub 3066 G=0.5160 A=0.4840
gnomAD - Genomes Other Sub 2022 G=0.7483 A=0.2517
14KJPN JAPANESE Study-wide 28034 G=0.66309 A=0.33691
Allele Frequency Aggregator Total Global 25740 G=0.80466 A=0.19483, C=0.00000, T=0.00051
Allele Frequency Aggregator European Sub 21210 G=0.78260 A=0.21678, C=0.00000, T=0.00061
Allele Frequency Aggregator African Sub 2298 G=0.9795 A=0.0205, C=0.0000, T=0.0000
Allele Frequency Aggregator Other Sub 1626 G=0.7989 A=0.2011, C=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 392 G=0.952 A=0.048, C=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 112 G=0.946 A=0.054, C=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 54 G=0.83 A=0.17, C=0.00, T=0.00
Allele Frequency Aggregator Asian Sub 48 G=0.81 A=0.19, C=0.00, T=0.00
8.3KJPN JAPANESE Study-wide 16590 G=0.66275 A=0.33725
1000Genomes_30x Global Study-wide 6404 G=0.7078 A=0.2922
1000Genomes_30x African Sub 1786 G=0.8488 A=0.1512
1000Genomes_30x Europe Sub 1266 G=0.7457 A=0.2543
1000Genomes_30x South Asian Sub 1202 G=0.5724 A=0.4276
1000Genomes_30x East Asian Sub 1170 G=0.5701 A=0.4299
1000Genomes_30x American Sub 980 G=0.733 A=0.267
1000Genomes Global Study-wide 5008 G=0.7029 A=0.2971
1000Genomes African Sub 1322 G=0.8449 A=0.1551
1000Genomes East Asian Sub 1008 G=0.5774 A=0.4226
1000Genomes Europe Sub 1006 G=0.7376 A=0.2624
1000Genomes South Asian Sub 978 G=0.582 A=0.418
1000Genomes American Sub 694 G=0.735 A=0.265
Genetic variation in the Estonian population Estonian Study-wide 4344 G=0.7366 A=0.2634
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7172 A=0.2828
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7298 A=0.2702
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.5956 A=0.4044, C=0.0000
Korean Genome Project KOREAN Study-wide 1832 G=0.5983 A=0.4017
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.699 A=0.301
Northern Sweden ACPOP Study-wide 562 G=0.817 A=0.183
SGDP_PRJ Global Study-wide 252 G=0.345 A=0.655
Qatari Global Study-wide 216 G=0.755 A=0.245
The Danish reference pan genome Danish Study-wide 40 G=0.88 A=0.12
Siberian Global Study-wide 30 G=0.50 A=0.50
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 2 NC_000002.12:g.32100345G>A
GRCh38.p14 chr 2 NC_000002.12:g.32100345G>C
GRCh38.p14 chr 2 NC_000002.12:g.32100345G>T
GRCh37.p13 chr 2 NC_000002.11:g.32325414G>A
GRCh37.p13 chr 2 NC_000002.11:g.32325414G>C
GRCh37.p13 chr 2 NC_000002.11:g.32325414G>T
SPAST RefSeqGene (LRG_714) NG_008730.1:g.41735G>A
SPAST RefSeqGene (LRG_714) NG_008730.1:g.41735G>C
SPAST RefSeqGene (LRG_714) NG_008730.1:g.41735G>T
Gene: SPAST, spastin (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SPAST transcript variant 3 NM_001363823.2:c.679+1454…

NM_001363823.2:c.679+1454G>A

N/A Intron Variant
SPAST transcript variant 4 NM_001363875.2:c.583+1074…

NM_001363875.2:c.583+10740G>A

N/A Intron Variant
SPAST transcript variant 5 NM_001377959.1:c.586+1074…

NM_001377959.1:c.586+10740G>A

N/A Intron Variant
SPAST transcript variant 1 NM_014946.4:c.682+1454G>A N/A Intron Variant
SPAST transcript variant 2 NM_199436.2:c.586+10740G>A N/A Intron 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 G= A C T
GRCh38.p14 chr 2 NC_000002.12:g.32100345= NC_000002.12:g.32100345G>A NC_000002.12:g.32100345G>C NC_000002.12:g.32100345G>T
GRCh37.p13 chr 2 NC_000002.11:g.32325414= NC_000002.11:g.32325414G>A NC_000002.11:g.32325414G>C NC_000002.11:g.32325414G>T
SPAST RefSeqGene (LRG_714) NG_008730.1:g.41735= NG_008730.1:g.41735G>A NG_008730.1:g.41735G>C NG_008730.1:g.41735G>T
SPAST transcript variant 3 NM_001363823.2:c.679+1454= NM_001363823.2:c.679+1454G>A NM_001363823.2:c.679+1454G>C NM_001363823.2:c.679+1454G>T
SPAST transcript variant 4 NM_001363875.2:c.583+10740= NM_001363875.2:c.583+10740G>A NM_001363875.2:c.583+10740G>C NM_001363875.2:c.583+10740G>T
SPAST transcript variant 5 NM_001377959.1:c.586+10740= NM_001377959.1:c.586+10740G>A NM_001377959.1:c.586+10740G>C NM_001377959.1:c.586+10740G>T
SPAST transcript variant 1 NM_014946.3:c.682+1454= NM_014946.3:c.682+1454G>A NM_014946.3:c.682+1454G>C NM_014946.3:c.682+1454G>T
SPAST transcript variant 1 NM_014946.4:c.682+1454= NM_014946.4:c.682+1454G>A NM_014946.4:c.682+1454G>C NM_014946.4:c.682+1454G>T
SPAST transcript variant 2 NM_199436.1:c.586+10740= NM_199436.1:c.586+10740G>A NM_199436.1:c.586+10740G>C NM_199436.1:c.586+10740G>T
SPAST transcript variant 2 NM_199436.2:c.586+10740= NM_199436.2:c.586+10740G>A NM_199436.2:c.586+10740G>C NM_199436.2:c.586+10740G>T
SPAST transcript variant X1 XM_005264516.1:c.679+1454= XM_005264516.1:c.679+1454G>A XM_005264516.1:c.679+1454G>C XM_005264516.1:c.679+1454G>T
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#.

65 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 ABI ss44251878 Mar 14, 2006 (126)
2 HGSV ss83162537 Dec 14, 2007 (130)
3 HUMANGENOME_JCVI ss97024952 Feb 04, 2009 (130)
4 ENSEMBL ss144239521 Dec 01, 2009 (131)
5 GMI ss156869007 Dec 01, 2009 (131)
6 1000GENOMES ss219152766 Jul 14, 2010 (132)
7 1000GENOMES ss231099289 Jul 14, 2010 (132)
8 1000GENOMES ss238670022 Jul 15, 2010 (132)
9 GMI ss276406039 May 04, 2012 (137)
10 GMI ss284318218 Apr 25, 2013 (138)
11 PJP ss292538300 May 09, 2011 (134)
12 ILLUMINA ss479928462 May 04, 2012 (137)
13 ILLUMINA ss484065607 May 04, 2012 (137)
14 ILLUMINA ss533400319 Sep 08, 2015 (146)
15 SSMP ss649035516 Apr 25, 2013 (138)
16 ILLUMINA ss779074759 Sep 08, 2015 (146)
17 ILLUMINA ss781103756 Sep 08, 2015 (146)
18 ILLUMINA ss834538387 Sep 08, 2015 (146)
19 EVA-GONL ss976649569 Aug 21, 2014 (142)
20 1000GENOMES ss1296532897 Aug 21, 2014 (142)
21 EVA_GENOME_DK ss1578805066 Apr 01, 2015 (144)
22 EVA_DECODE ss1586056650 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1603142077 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1646136110 Apr 01, 2015 (144)
25 WEILL_CORNELL_DGM ss1919882082 Feb 12, 2016 (147)
26 JJLAB ss2020470368 Sep 14, 2016 (149)
27 USC_VALOUEV ss2148514689 Dec 20, 2016 (150)
28 SYSTEMSBIOZJU ss2624749206 Nov 08, 2017 (151)
29 ILLUMINA ss2633592309 Nov 08, 2017 (151)
30 GRF ss2703076090 Nov 08, 2017 (151)
31 GNOMAD ss2771485120 Nov 08, 2017 (151)
32 SWEGEN ss2989226564 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3024001548 Nov 08, 2017 (151)
34 CSHL ss3344145906 Nov 08, 2017 (151)
35 ILLUMINA ss3628027103 Oct 11, 2018 (152)
36 ILLUMINA ss3631560586 Oct 11, 2018 (152)
37 URBANLAB ss3646998439 Oct 11, 2018 (152)
38 EGCUT_WGS ss3657183872 Jul 13, 2019 (153)
39 EVA_DECODE ss3703555067 Jul 13, 2019 (153)
40 ACPOP ss3728285858 Jul 13, 2019 (153)
41 EVA ss3756546367 Jul 13, 2019 (153)
42 PACBIO ss3783820163 Jul 13, 2019 (153)
43 PACBIO ss3789414667 Jul 13, 2019 (153)
44 PACBIO ss3794287430 Jul 13, 2019 (153)
45 KHV_HUMAN_GENOMES ss3800924220 Jul 13, 2019 (153)
46 EVA ss3826897197 Apr 25, 2020 (154)
47 EVA ss3836856328 Apr 25, 2020 (154)
48 EVA ss3842271050 Apr 25, 2020 (154)
49 SGDP_PRJ ss3851911709 Apr 25, 2020 (154)
50 KRGDB ss3897333791 Apr 25, 2020 (154)
51 KOGIC ss3947422229 Apr 25, 2020 (154)
52 TOPMED ss4499559069 Apr 26, 2021 (155)
53 TOMMO_GENOMICS ss5150570599 Apr 26, 2021 (155)
54 1000G_HIGH_COVERAGE ss5247456324 Oct 17, 2022 (156)
55 EVA ss5314722096 Oct 17, 2022 (156)
56 HUGCELL_USP ss5447715412 Oct 17, 2022 (156)
57 EVA ss5506344423 Oct 17, 2022 (156)
58 1000G_HIGH_COVERAGE ss5522354374 Oct 17, 2022 (156)
59 SANFORD_IMAGENETICS ss5628399156 Oct 17, 2022 (156)
60 TOMMO_GENOMICS ss5678966327 Oct 17, 2022 (156)
61 YY_MCH ss5802056160 Oct 17, 2022 (156)
62 EVA ss5819864171 Oct 17, 2022 (156)
63 EVA ss5852453074 Oct 17, 2022 (156)
64 EVA ss5929658017 Oct 17, 2022 (156)
65 EVA ss5954606374 Oct 17, 2022 (156)
66 1000Genomes NC_000002.11 - 32325414 Oct 11, 2018 (152)
67 1000Genomes_30x NC_000002.12 - 32100345 Oct 17, 2022 (156)
68 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 32325414 Oct 11, 2018 (152)
69 Genetic variation in the Estonian population NC_000002.11 - 32325414 Oct 11, 2018 (152)
70 The Danish reference pan genome NC_000002.11 - 32325414 Apr 25, 2020 (154)
71 gnomAD - Genomes NC_000002.12 - 32100345 Apr 26, 2021 (155)
72 Genome of the Netherlands Release 5 NC_000002.11 - 32325414 Apr 25, 2020 (154)
73 KOREAN population from KRGDB NC_000002.11 - 32325414 Apr 25, 2020 (154)
74 Korean Genome Project NC_000002.12 - 32100345 Apr 25, 2020 (154)
75 Northern Sweden NC_000002.11 - 32325414 Jul 13, 2019 (153)
76 Qatari NC_000002.11 - 32325414 Apr 25, 2020 (154)
77 SGDP_PRJ NC_000002.11 - 32325414 Apr 25, 2020 (154)
78 Siberian NC_000002.11 - 32325414 Apr 25, 2020 (154)
79 8.3KJPN NC_000002.11 - 32325414 Apr 26, 2021 (155)
80 14KJPN NC_000002.12 - 32100345 Oct 17, 2022 (156)
81 TopMed NC_000002.12 - 32100345 Apr 26, 2021 (155)
82 UK 10K study - Twins NC_000002.11 - 32325414 Oct 11, 2018 (152)
83 ALFA NC_000002.12 - 32100345 Apr 26, 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)
rs57204402 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss83162537 NC_000002.9:32237064:G:A NC_000002.12:32100344:G:A (self)
ss276406039, ss284318218, ss292538300, ss484065607, ss1586056650 NC_000002.10:32178917:G:A NC_000002.12:32100344:G:A (self)
7455689, 4140839, 2922120, 4980470, 1818115, 4511185, 1570723, 1924012, 3928689, 1031043, 8539906, 4140839, ss219152766, ss231099289, ss238670022, ss479928462, ss533400319, ss649035516, ss779074759, ss781103756, ss834538387, ss976649569, ss1296532897, ss1578805066, ss1603142077, ss1646136110, ss1919882082, ss2020470368, ss2148514689, ss2624749206, ss2633592309, ss2703076090, ss2771485120, ss2989226564, ss3344145906, ss3628027103, ss3631560586, ss3657183872, ss3728285858, ss3756546367, ss3783820163, ss3789414667, ss3794287430, ss3826897197, ss3836856328, ss3851911709, ss3897333791, ss5150570599, ss5314722096, ss5506344423, ss5628399156, ss5819864171, ss5954606374 NC_000002.11:32325413:G:A NC_000002.12:32100344:G:A (self)
9880309, 52957849, 3800230, 12803431, 303381948, 6532967883, ss3024001548, ss3646998439, ss3703555067, ss3800924220, ss3842271050, ss3947422229, ss4499559069, ss5247456324, ss5447715412, ss5522354374, ss5678966327, ss5802056160, ss5852453074, ss5929658017 NC_000002.12:32100344:G:A NC_000002.12:32100344:G:A (self)
ss44251878, ss97024952, ss144239521, ss156869007 NT_022184.15:11147300:G:A NC_000002.12:32100344:G:A (self)
4511185, ss3897333791 NC_000002.11:32325413:G:C NC_000002.12:32100344:G:C (self)
6532967883 NC_000002.12:32100344:G:C NC_000002.12:32100344:G:C (self)
ss2771485120 NC_000002.11:32325413:G:T NC_000002.12:32100344:G:T (self)
6532967883 NC_000002.12:32100344:G:T NC_000002.12:32100344:G:T (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 rs34835885

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