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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.

rs309375

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr4:122760001 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.263894 (69850/264690, TOPMED)
C=0.303716 (42533/140042, GnomAD)
C=0.39487 (23632/59848, ALFA) (+ 17 more)
C=0.01921 (322/16760, 8.3KJPN)
C=0.1701 (852/5008, 1000G)
A=0.4967 (2225/4480, Estonian)
C=0.4338 (1672/3854, ALSPAC)
C=0.4304 (1596/3708, TWINSUK)
C=0.0321 (94/2930, KOREAN)
C=0.1588 (331/2084, HGDP_Stanford)
C=0.1317 (235/1784, HapMap)
C=0.475 (474/998, GoNL)
C=0.058 (46/792, PRJEB37584)
C=0.383 (230/600, NorthernSweden)
C=0.135 (73/540, SGDP_PRJ)
C=0.167 (36/216, Qatari)
C=0.070 (15/214, Vietnamese)
C=0.44 (24/54, Ancient Sardinia)
C=0.25 (12/48, Siberian)
A=0.45 (18/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 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 4 NC_000004.12:g.122760001C>A
GRCh38.p13 chr 4 NC_000004.12:g.122760001C>G
GRCh38.p13 chr 4 NC_000004.12:g.122760001C>T
GRCh37.p13 chr 4 NC_000004.11:g.123681156C>A
GRCh37.p13 chr 4 NC_000004.11:g.123681156C>G
GRCh37.p13 chr 4 NC_000004.11:g.123681156C>T
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

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 59848 C=0.39487 A=0.60513, T=0.00000
European Sub 50880 C=0.43514 A=0.56486, T=0.00000
African Sub 2244 C=0.0731 A=0.9269, T=0.0000
African Others Sub 86 C=0.02 A=0.98, T=0.00
African American Sub 2158 C=0.0751 A=0.9249, T=0.0000
Asian Sub 84 C=0.10 A=0.90, T=0.00
East Asian Sub 66 C=0.09 A=0.91, T=0.00
Other Asian Sub 18 C=0.11 A=0.89, T=0.00
Latin American 1 Sub 120 C=0.383 A=0.617, T=0.000
Latin American 2 Sub 660 C=0.330 A=0.670, T=0.000
South Asian Sub 4864 C=0.1513 A=0.8487, T=0.0000
Other Sub 996 C=0.321 A=0.679, T=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 C=0.263894 A=0.736106
gnomAD - Genomes Global Study-wide 140042 C=0.303716 A=0.696284
gnomAD - Genomes European Sub 75790 C=0.44644 A=0.55356
gnomAD - Genomes African Sub 42012 C=0.07819 A=0.92181
gnomAD - Genomes American Sub 13638 C=0.27915 A=0.72085
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.2434 A=0.7566
gnomAD - Genomes East Asian Sub 3132 C=0.0546 A=0.9454
gnomAD - Genomes Other Sub 2146 C=0.2912 A=0.7088
8.3KJPN JAPANESE Study-wide 16760 C=0.01921 A=0.98079
1000Genomes Global Study-wide 5008 C=0.1701 A=0.8299
1000Genomes African Sub 1322 C=0.0212 A=0.9788
1000Genomes East Asian Sub 1008 C=0.0496 A=0.9504
1000Genomes Europe Sub 1006 C=0.4493 A=0.5507
1000Genomes South Asian Sub 978 C=0.142 A=0.858
1000Genomes American Sub 694 C=0.264 A=0.736
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5033 A=0.4967
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.4338 A=0.5662
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.4304 A=0.5696
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.0321 A=0.9679, G=0.0000
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 C=0.1588 A=0.8412
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 C=0.064 A=0.936
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 C=0.152 A=0.848
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 C=0.200 A=0.800
HGDP-CEPH-db Supplement 1 Europe Sub 320 C=0.412 A=0.588
HGDP-CEPH-db Supplement 1 Africa Sub 242 C=0.004 A=0.996
HGDP-CEPH-db Supplement 1 America Sub 216 C=0.042 A=0.958
HGDP-CEPH-db Supplement 1 Oceania Sub 72 C=0.36 A=0.64
HapMap Global Study-wide 1784 C=0.1317 A=0.8683
HapMap American Sub 770 C=0.208 A=0.792
HapMap African Sub 584 C=0.007 A=0.993
HapMap Asian Sub 254 C=0.039 A=0.961
HapMap Europe Sub 176 C=0.347 A=0.653
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.475 A=0.525
CNV burdens in cranial meningiomas Global Study-wide 792 C=0.058 A=0.942
CNV burdens in cranial meningiomas CRM Sub 792 C=0.058 A=0.942
Northern Sweden ACPOP Study-wide 600 C=0.383 A=0.617
SGDP_PRJ Global Study-wide 540 C=0.135 A=0.865
Qatari Global Study-wide 216 C=0.167 A=0.833
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.070 A=0.930
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 54 C=0.44 A=0.56
Siberian Global Study-wide 48 C=0.25 A=0.75
The Danish reference pan genome Danish Study-wide 40 C=0.55 A=0.45
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 C= A G T
GRCh38.p13 chr 4 NC_000004.12:g.122760001= NC_000004.12:g.122760001C>A NC_000004.12:g.122760001C>G NC_000004.12:g.122760001C>T
GRCh37.p13 chr 4 NC_000004.11:g.123681156= NC_000004.11:g.123681156C>A NC_000004.11:g.123681156C>G NC_000004.11:g.123681156C>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#.

94 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss397587 Jul 12, 2000 (79)
2 SC_JCM ss486896 Jul 16, 2000 (80)
3 KWOK ss914546 Oct 04, 2000 (86)
4 KWOK ss1583318 Oct 18, 2000 (87)
5 WI_SSAHASNP ss14622028 Dec 05, 2003 (119)
6 SSAHASNP ss22136563 Apr 05, 2004 (121)
7 PERLEGEN ss24347858 Sep 20, 2004 (123)
8 ABI ss44533009 Mar 13, 2006 (126)
9 ILLUMINA ss66713558 Nov 29, 2006 (127)
10 ILLUMINA ss67289571 Nov 29, 2006 (127)
11 ILLUMINA ss67692945 Nov 29, 2006 (127)
12 ILLUMINA ss70768145 May 25, 2008 (130)
13 ILLUMINA ss71343063 May 16, 2007 (127)
14 ILLUMINA ss75637324 Dec 07, 2007 (129)
15 HGSV ss78619702 Dec 07, 2007 (129)
16 ILLUMINA ss79157893 Dec 15, 2007 (130)
17 HGSV ss81996974 Dec 15, 2007 (130)
18 KRIBB_YJKIM ss83421847 Dec 15, 2007 (130)
19 BCMHGSC_JDW ss92757119 Mar 24, 2008 (129)
20 HUMANGENOME_JCVI ss98859251 Feb 05, 2009 (130)
21 BGI ss105859069 Feb 05, 2009 (130)
22 1000GENOMES ss108297975 Jan 23, 2009 (130)
23 1000GENOMES ss110521212 Jan 24, 2009 (130)
24 ILLUMINA-UK ss117171599 Feb 14, 2009 (130)
25 ILLUMINA ss122167537 Dec 01, 2009 (131)
26 ENSEMBL ss135155086 Dec 01, 2009 (131)
27 ENSEMBL ss139859008 Dec 01, 2009 (131)
28 ILLUMINA ss154253115 Dec 01, 2009 (131)
29 GMI ss157842112 Dec 01, 2009 (131)
30 ILLUMINA ss159430009 Dec 01, 2009 (131)
31 COMPLETE_GENOMICS ss164240711 Jul 04, 2010 (132)
32 COMPLETE_GENOMICS ss167111767 Jul 04, 2010 (132)
33 ILLUMINA ss171532807 Jul 04, 2010 (132)
34 ILLUMINA ss173559356 Jul 04, 2010 (132)
35 BUSHMAN ss199117017 Jul 04, 2010 (132)
36 BCM-HGSC-SUB ss206530751 Jul 04, 2010 (132)
37 1000GENOMES ss232579019 Jul 14, 2010 (132)
38 1000GENOMES ss239829128 Jul 15, 2010 (132)
39 GMI ss277908316 May 04, 2012 (137)
40 PJP ss293178628 May 09, 2011 (134)
41 ILLUMINA ss537160417 Sep 08, 2015 (146)
42 TISHKOFF ss557822360 Apr 25, 2013 (138)
43 SSMP ss651632042 Apr 25, 2013 (138)
44 ILLUMINA ss825488411 Apr 01, 2015 (144)
45 ILLUMINA ss832941618 Aug 21, 2014 (142)
46 ILLUMINA ss833532448 Aug 21, 2014 (142)
47 EVA-GONL ss980623929 Aug 21, 2014 (142)
48 JMKIDD_LAB ss1071916626 Aug 21, 2014 (142)
49 1000GENOMES ss1311618701 Aug 21, 2014 (142)
50 DDI ss1430034405 Apr 01, 2015 (144)
51 EVA_GENOME_DK ss1580755453 Apr 01, 2015 (144)
52 EVA_DECODE ss1590131739 Apr 01, 2015 (144)
53 EVA_UK10K_ALSPAC ss1611074144 Apr 01, 2015 (144)
54 EVA_UK10K_TWINSUK ss1654068177 Apr 01, 2015 (144)
55 EVA_SVP ss1712703836 Apr 01, 2015 (144)
56 HAMMER_LAB ss1802131356 Sep 08, 2015 (146)
57 WEILL_CORNELL_DGM ss1923866681 Feb 12, 2016 (147)
58 GENOMED ss1969855944 Jul 19, 2016 (147)
59 JJLAB ss2022516683 Sep 14, 2016 (149)
60 USC_VALOUEV ss2150647757 Dec 20, 2016 (150)
61 HUMAN_LONGEVITY ss2266742446 Dec 20, 2016 (150)
62 TOPMED ss2434611895 Dec 20, 2016 (150)
63 SYSTEMSBIOZJU ss2625755131 Nov 08, 2017 (151)
64 GRF ss2706131509 Nov 08, 2017 (151)
65 GNOMAD ss2814694277 Nov 08, 2017 (151)
66 SWEGEN ss2995474705 Nov 08, 2017 (151)
67 BIOINF_KMB_FNS_UNIBA ss3025035475 Nov 08, 2017 (151)
68 CSHL ss3345938253 Nov 08, 2017 (151)
69 TOPMED ss3441475378 Nov 08, 2017 (151)
70 ILLUMINA ss3629057216 Oct 12, 2018 (152)
71 ILLUMINA ss3638509745 Oct 12, 2018 (152)
72 ILLUMINA ss3639257112 Oct 12, 2018 (152)
73 ILLUMINA ss3639650222 Oct 12, 2018 (152)
74 ILLUMINA ss3643459347 Oct 12, 2018 (152)
75 URBANLAB ss3647838043 Oct 12, 2018 (152)
76 EGCUT_WGS ss3663377467 Jul 13, 2019 (153)
77 EVA_DECODE ss3712968486 Jul 13, 2019 (153)
78 ACPOP ss3731565618 Jul 13, 2019 (153)
79 EVA ss3762353061 Jul 13, 2019 (153)
80 PACBIO ss3784846425 Jul 13, 2019 (153)
81 PACBIO ss3790284393 Jul 13, 2019 (153)
82 PACBIO ss3795159855 Jul 13, 2019 (153)
83 KHV_HUMAN_GENOMES ss3805508432 Jul 13, 2019 (153)
84 EVA ss3828784324 Apr 26, 2020 (154)
85 EVA ss3837836686 Apr 26, 2020 (154)
86 EVA ss3843275877 Apr 26, 2020 (154)
87 HGDP ss3847763585 Apr 26, 2020 (154)
88 SGDP_PRJ ss3859950415 Apr 26, 2020 (154)
89 KRGDB ss3906251622 Apr 26, 2020 (154)
90 EVA ss3984534472 Apr 26, 2021 (155)
91 EVA ss3985093618 Apr 26, 2021 (155)
92 EVA ss4017166808 Apr 26, 2021 (155)
93 TOPMED ss4630288868 Apr 26, 2021 (155)
94 TOMMO_GENOMICS ss5167784018 Apr 26, 2021 (155)
95 1000Genomes NC_000004.11 - 123681156 Oct 12, 2018 (152)
96 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 123681156 Oct 12, 2018 (152)
97 Genetic variation in the Estonian population NC_000004.11 - 123681156 Oct 12, 2018 (152)
98 The Danish reference pan genome NC_000004.11 - 123681156 Apr 26, 2020 (154)
99 gnomAD - Genomes NC_000004.12 - 122760001 Apr 26, 2021 (155)
100 Genome of the Netherlands Release 5 NC_000004.11 - 123681156 Apr 26, 2020 (154)
101 HGDP-CEPH-db Supplement 1 NC_000004.10 - 123900606 Apr 26, 2020 (154)
102 HapMap NC_000004.12 - 122760001 Apr 26, 2020 (154)
103 KOREAN population from KRGDB NC_000004.11 - 123681156 Apr 26, 2020 (154)
104 Northern Sweden NC_000004.11 - 123681156 Jul 13, 2019 (153)
105 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000004.11 - 123681156 Apr 26, 2021 (155)
106 CNV burdens in cranial meningiomas NC_000004.11 - 123681156 Apr 26, 2021 (155)
107 Qatari NC_000004.11 - 123681156 Apr 26, 2020 (154)
108 SGDP_PRJ NC_000004.11 - 123681156 Apr 26, 2020 (154)
109 Siberian NC_000004.11 - 123681156 Apr 26, 2020 (154)
110 8.3KJPN NC_000004.11 - 123681156 Apr 26, 2021 (155)
111 TopMed NC_000004.12 - 122760001 Apr 26, 2021 (155)
112 UK 10K study - Twins NC_000004.11 - 123681156 Oct 12, 2018 (152)
113 A Vietnamese Genetic Variation Database NC_000004.11 - 123681156 Jul 13, 2019 (153)
114 ALFA NC_000004.12 - 122760001 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)
rs17472104 Oct 07, 2004 (123)
rs59531867 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78619702, ss81996974, ss3639257112, ss3639650222 NC_000004.9:124038760:C:A NC_000004.12:122760000:C:A (self)
441477, ss92757119, ss108297975, ss110521212, ss117171599, ss164240711, ss167111767, ss199117017, ss206530751, ss277908316, ss293178628, ss825488411, ss1590131739, ss1712703836, ss3643459347, ss3847763585 NC_000004.10:123900605:C:A NC_000004.12:122760000:C:A (self)
23086109, 12843805, 9115715, 6920392, 5683315, 13429016, 4850483, 319545, 83833, 5908611, 11967395, 3164111, 25753325, 12843805, 2826037, ss232579019, ss239829128, ss537160417, ss557822360, ss651632042, ss832941618, ss833532448, ss980623929, ss1071916626, ss1311618701, ss1430034405, ss1580755453, ss1611074144, ss1654068177, ss1802131356, ss1923866681, ss1969855944, ss2022516683, ss2150647757, ss2434611895, ss2625755131, ss2706131509, ss2814694277, ss2995474705, ss3345938253, ss3629057216, ss3638509745, ss3663377467, ss3731565618, ss3762353061, ss3784846425, ss3790284393, ss3795159855, ss3828784324, ss3837836686, ss3859950415, ss3906251622, ss3984534472, ss3985093618, ss4017166808, ss5167784018 NC_000004.11:123681155:C:A NC_000004.12:122760000:C:A (self)
163537503, 2701238, 292347684, 467666424, 11787290388, ss2266742446, ss3025035475, ss3441475378, ss3647838043, ss3712968486, ss3805508432, ss3843275877, ss4630288868 NC_000004.12:122760000:C:A NC_000004.12:122760000:C:A (self)
ss14622028, ss22136563 NT_016354.16:48176286:C:A NC_000004.12:122760000:C:A (self)
ss397587, ss486896, ss914546, ss1583318, ss24347858, ss44533009, ss66713558, ss67289571, ss67692945, ss70768145, ss71343063, ss75637324, ss79157893, ss83421847, ss98859251, ss105859069, ss122167537, ss135155086, ss139859008, ss154253115, ss157842112, ss159430009, ss171532807, ss173559356 NT_016354.19:48228876:C:A NC_000004.12:122760000:C:A (self)
13429016, ss3906251622 NC_000004.11:123681155:C:G NC_000004.12:122760000:C:G (self)
11787290388 NC_000004.12:122760000:C:T NC_000004.12:122760000:C:T
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 rs309375

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