Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs35325987

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:137473354 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.025369 (6715/264690, TOPMED)
G=0.025698 (3605/140284, GnomAD)
G=0.02372 (1867/78700, PAGE_STUDY) (+ 14 more)
G=0.02213 (422/19072, ALFA)
G=0.0175 (112/6404, 1000G_30x)
G=0.0166 (83/5008, 1000G)
G=0.0174 (78/4480, Estonian)
G=0.0210 (81/3854, ALSPAC)
G=0.0208 (77/3708, TWINSUK)
G=0.015 (15/998, GoNL)
G=0.052 (31/600, NorthernSweden)
G=0.028 (6/216, Qatari)
G=0.03 (1/40, GENOME_DK)
A=0.50 (8/16, SGDP_PRJ)
G=0.50 (8/16, SGDP_PRJ)
A=0.5 (1/2, Siberian)
G=0.5 (1/2, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SPOCK1 : 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 19072 A=0.97787 G=0.02213
European Sub 14364 A=0.97946 G=0.02054
African Sub 2954 A=0.9665 G=0.0335
African Others Sub 114 A=0.982 G=0.018
African American Sub 2840 A=0.9658 G=0.0342
Asian Sub 146 A=1.000 G=0.000
East Asian Sub 120 A=1.000 G=0.000
Other Asian Sub 26 A=1.00 G=0.00
Latin American 1 Sub 146 A=0.993 G=0.007
Latin American 2 Sub 610 A=0.982 G=0.018
South Asian Sub 104 A=0.990 G=0.010
Other Sub 748 A=0.980 G=0.020


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 A=0.974631 G=0.025369
gnomAD - Genomes Global Study-wide 140284 A=0.974302 G=0.025698
gnomAD - Genomes European Sub 75958 A=0.97844 G=0.02156
gnomAD - Genomes African Sub 42050 A=0.96507 G=0.03493
gnomAD - Genomes American Sub 13666 A=0.98076 G=0.01924
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.9492 G=0.0508
gnomAD - Genomes East Asian Sub 3132 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 A=0.9694 G=0.0306
The PAGE Study Global Study-wide 78700 A=0.97628 G=0.02372
The PAGE Study AfricanAmerican Sub 32514 A=0.96217 G=0.03783
The PAGE Study Mexican Sub 10810 A=0.98659 G=0.01341
The PAGE Study Asian Sub 8318 A=1.0000 G=0.0000
The PAGE Study PuertoRican Sub 7918 A=0.9848 G=0.0152
The PAGE Study NativeHawaiian Sub 4534 A=0.9945 G=0.0055
The PAGE Study Cuban Sub 4230 A=0.9704 G=0.0296
The PAGE Study Dominican Sub 3828 A=0.9713 G=0.0287
The PAGE Study CentralAmerican Sub 2450 A=0.9792 G=0.0208
The PAGE Study SouthAmerican Sub 1982 A=0.9834 G=0.0166
The PAGE Study NativeAmerican Sub 1260 A=0.9794 G=0.0206
The PAGE Study SouthAsian Sub 856 A=0.998 G=0.002
Allele Frequency Aggregator Total Global 19072 A=0.97787 G=0.02213
Allele Frequency Aggregator European Sub 14364 A=0.97946 G=0.02054
Allele Frequency Aggregator African Sub 2954 A=0.9665 G=0.0335
Allele Frequency Aggregator Other Sub 748 A=0.980 G=0.020
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.982 G=0.018
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.993 G=0.007
Allele Frequency Aggregator Asian Sub 146 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 104 A=0.990 G=0.010
1000Genomes_30x Global Study-wide 6404 A=0.9825 G=0.0175
1000Genomes_30x African Sub 1786 A=0.9681 G=0.0319
1000Genomes_30x Europe Sub 1266 A=0.9771 G=0.0229
1000Genomes_30x South Asian Sub 1202 A=0.9958 G=0.0042
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.979 G=0.021
1000Genomes Global Study-wide 5008 A=0.9834 G=0.0166
1000Genomes African Sub 1322 A=0.9682 G=0.0318
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=0.9771 G=0.0229
1000Genomes South Asian Sub 978 A=0.995 G=0.005
1000Genomes American Sub 694 A=0.981 G=0.019
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9826 G=0.0174
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9790 G=0.0210
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9792 G=0.0208
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.985 G=0.015
Northern Sweden ACPOP Study-wide 600 A=0.948 G=0.052
Qatari Global Study-wide 216 A=0.972 G=0.028
The Danish reference pan genome Danish Study-wide 40 A=0.97 G=0.03
SGDP_PRJ Global Study-wide 16 A=0.50 G=0.50
Siberian Global Study-wide 2 A=0.5 G=0.5
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 5 NC_000005.10:g.137473354A>G
GRCh37.p13 chr 5 NC_000005.9:g.136809043A>G
SPOCK1 RefSeqGene NG_034127.1:g.30976T>C
Gene: SPOCK1, SPARC (osteonectin), cwcv and kazal like domains proteoglycan 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SPOCK1 transcript NM_004598.4:c.186+25019T>C 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 A= G
GRCh38.p14 chr 5 NC_000005.10:g.137473354= NC_000005.10:g.137473354A>G
GRCh37.p13 chr 5 NC_000005.9:g.136809043= NC_000005.9:g.136809043A>G
SPOCK1 RefSeqGene NG_034127.1:g.30976= NG_034127.1:g.30976T>C
SPOCK1 transcript NM_004598.3:c.186+25019= NM_004598.3:c.186+25019T>C
SPOCK1 transcript NM_004598.4:c.186+25019= NM_004598.4:c.186+25019T>C
SPOCK1 transcript variant X1 XM_005272067.1:c.186+25019= XM_005272067.1:c.186+25019T>C
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#.

36 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 ABI ss42505465 Mar 14, 2006 (126)
2 1000GENOMES ss221989569 Jul 14, 2010 (132)
3 1000GENOMES ss233165826 Jul 14, 2010 (132)
4 TISHKOFF ss558740244 Apr 25, 2013 (138)
5 EVA-GONL ss982168063 Aug 21, 2014 (142)
6 1000GENOMES ss1317387463 Aug 21, 2014 (142)
7 EVA_GENOME_DK ss1581367772 Apr 01, 2015 (144)
8 EVA_DECODE ss1591696595 Apr 01, 2015 (144)
9 EVA_UK10K_ALSPAC ss1614104086 Apr 01, 2015 (144)
10 EVA_UK10K_TWINSUK ss1657098119 Apr 01, 2015 (144)
11 WEILL_CORNELL_DGM ss1925424717 Feb 12, 2016 (147)
12 ILLUMINA ss1958825493 Feb 12, 2016 (147)
13 USC_VALOUEV ss2151475282 Dec 20, 2016 (150)
14 HUMAN_LONGEVITY ss2278510516 Dec 20, 2016 (150)
15 GNOMAD ss2831254667 Nov 08, 2017 (151)
16 SWEGEN ss2997859278 Nov 08, 2017 (151)
17 ILLUMINA ss3022533085 Nov 08, 2017 (151)
18 CSHL ss3346647063 Nov 08, 2017 (151)
19 URBANLAB ss3648178538 Oct 12, 2018 (152)
20 ILLUMINA ss3653035254 Oct 12, 2018 (152)
21 EGCUT_WGS ss3665774962 Jul 13, 2019 (153)
22 EVA_DECODE ss3715781981 Jul 13, 2019 (153)
23 ILLUMINA ss3726273540 Jul 13, 2019 (153)
24 ACPOP ss3732853097 Jul 13, 2019 (153)
25 PAGE_CC ss3771233413 Jul 13, 2019 (153)
26 SGDP_PRJ ss3863064285 Apr 26, 2020 (154)
27 TOPMED ss4680190657 Apr 26, 2021 (155)
28 1000G_HIGH_COVERAGE ss5265991315 Oct 17, 2022 (156)
29 EVA ss5361238874 Oct 17, 2022 (156)
30 HUGCELL_USP ss5463943414 Oct 17, 2022 (156)
31 EVA ss5508230309 Oct 17, 2022 (156)
32 1000G_HIGH_COVERAGE ss5550716905 Oct 17, 2022 (156)
33 SANFORD_IMAGENETICS ss5638967795 Oct 17, 2022 (156)
34 EVA ss5835699147 Oct 17, 2022 (156)
35 EVA ss5896494663 Oct 17, 2022 (156)
36 EVA ss5967439080 Oct 17, 2022 (156)
37 1000Genomes NC_000005.9 - 136809043 Oct 12, 2018 (152)
38 1000Genomes_30x NC_000005.10 - 137473354 Oct 17, 2022 (156)
39 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 136809043 Oct 12, 2018 (152)
40 Genetic variation in the Estonian population NC_000005.9 - 136809043 Oct 12, 2018 (152)
41 The Danish reference pan genome NC_000005.9 - 136809043 Apr 26, 2020 (154)
42 gnomAD - Genomes NC_000005.10 - 137473354 Apr 26, 2021 (155)
43 Genome of the Netherlands Release 5 NC_000005.9 - 136809043 Apr 26, 2020 (154)
44 Northern Sweden NC_000005.9 - 136809043 Jul 13, 2019 (153)
45 The PAGE Study NC_000005.10 - 137473354 Jul 13, 2019 (153)
46 Qatari NC_000005.9 - 136809043 Apr 26, 2020 (154)
47 SGDP_PRJ NC_000005.9 - 136809043 Apr 26, 2020 (154)
48 Siberian NC_000005.9 - 136809043 Apr 26, 2020 (154)
49 TopMed NC_000005.10 - 137473354 Apr 26, 2021 (155)
50 UK 10K study - Twins NC_000005.9 - 136809043 Oct 12, 2018 (152)
51 ALFA NC_000005.10 - 137473354 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1591696595 NC_000005.8:136836941:A:G NC_000005.10:137473353:A:G (self)
29071933, 16171902, 11513210, 7532711, 7186098, 6137962, 7466647, 15081265, 3991636, 16171902, ss221989569, ss233165826, ss558740244, ss982168063, ss1317387463, ss1581367772, ss1614104086, ss1657098119, ss1925424717, ss1958825493, ss2151475282, ss2831254667, ss2997859278, ss3022533085, ss3346647063, ss3653035254, ss3665774962, ss3732853097, ss3863064285, ss5361238874, ss5508230309, ss5638967795, ss5835699147, ss5967439080 NC_000005.9:136809042:A:G NC_000005.10:137473353:A:G (self)
38242840, 205601306, 454882, 517568214, 4739031564, ss2278510516, ss3648178538, ss3715781981, ss3726273540, ss3771233413, ss4680190657, ss5265991315, ss5463943414, ss5550716905, ss5896494663 NC_000005.10:137473353:A:G NC_000005.10:137473353:A:G (self)
ss42505465 NT_034772.6:45122914:A:G NC_000005.10:137473353:A:G (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 rs35325987

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