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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.

rs2303617

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:113273459 (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=0.088723 (23484/264690, TOPMED)
G=0.090772 (12723/140164, GnomAD)
G=0.28509 (8056/28258, 14KJPN) (+ 19 more)
G=0.07713 (1457/18890, ALFA)
G=0.28634 (4799/16760, 8.3KJPN)
G=0.1124 (720/6404, 1000G_30x)
G=0.1160 (581/5008, 1000G)
G=0.0605 (271/4480, Estonian)
G=0.0682 (263/3854, ALSPAC)
G=0.0769 (285/3708, TWINSUK)
G=0.2379 (697/2930, KOREAN)
G=0.2314 (424/1832, Korea1K)
G=0.064 (64/998, GoNL)
G=0.050 (30/600, NorthernSweden)
G=0.011 (6/534, MGP)
G=0.119 (39/328, HapMap)
G=0.083 (18/216, Qatari)
G=0.142 (30/212, Vietnamese)
A=0.387 (58/150, SGDP_PRJ)
G=0.12 (5/40, GENOME_DK)
A=0.50 (8/16, Siberian)
G=0.50 (8/16, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TPCN1 : 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 18890 A=0.92287 G=0.07713
European Sub 14286 A=0.93196 G=0.06804
African Sub 2946 A=0.8832 G=0.1168
African Others Sub 114 A=0.895 G=0.105
African American Sub 2832 A=0.8828 G=0.1172
Asian Sub 112 A=0.821 G=0.179
East Asian Sub 86 A=0.85 G=0.15
Other Asian Sub 26 A=0.73 G=0.27
Latin American 1 Sub 146 A=0.925 G=0.075
Latin American 2 Sub 610 A=0.925 G=0.075
South Asian Sub 98 A=0.94 G=0.06
Other Sub 692 A=0.916 G=0.084


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=0.911277 G=0.088723
gnomAD - Genomes Global Study-wide 140164 A=0.909228 G=0.090772
gnomAD - Genomes European Sub 75888 A=0.92001 G=0.07999
gnomAD - Genomes African Sub 42028 A=0.89362 G=0.10638
gnomAD - Genomes American Sub 13652 A=0.91862 G=0.08138
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=0.9226 G=0.0774
gnomAD - Genomes East Asian Sub 3122 A=0.8017 G=0.1983
gnomAD - Genomes Other Sub 2152 A=0.9094 G=0.0906
14KJPN JAPANESE Study-wide 28258 A=0.71491 G=0.28509
Allele Frequency Aggregator Total Global 18890 A=0.92287 G=0.07713
Allele Frequency Aggregator European Sub 14286 A=0.93196 G=0.06804
Allele Frequency Aggregator African Sub 2946 A=0.8832 G=0.1168
Allele Frequency Aggregator Other Sub 692 A=0.916 G=0.084
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.925 G=0.075
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.925 G=0.075
Allele Frequency Aggregator Asian Sub 112 A=0.821 G=0.179
Allele Frequency Aggregator South Asian Sub 98 A=0.94 G=0.06
8.3KJPN JAPANESE Study-wide 16760 A=0.71366 G=0.28634
1000Genomes_30x Global Study-wide 6404 A=0.8876 G=0.1124
1000Genomes_30x African Sub 1786 A=0.8953 G=0.1047
1000Genomes_30x Europe Sub 1266 A=0.9123 G=0.0877
1000Genomes_30x South Asian Sub 1202 A=0.9093 G=0.0907
1000Genomes_30x East Asian Sub 1170 A=0.7872 G=0.2128
1000Genomes_30x American Sub 980 A=0.935 G=0.065
1000Genomes Global Study-wide 5008 A=0.8840 G=0.1160
1000Genomes African Sub 1322 A=0.8971 G=0.1029
1000Genomes East Asian Sub 1008 A=0.7847 G=0.2153
1000Genomes Europe Sub 1006 A=0.9076 G=0.0924
1000Genomes South Asian Sub 978 A=0.909 G=0.091
1000Genomes American Sub 694 A=0.934 G=0.066
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9395 G=0.0605
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9318 G=0.0682
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9231 G=0.0769
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.7621 G=0.2379
Korean Genome Project KOREAN Study-wide 1832 A=0.7686 G=0.2314
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.936 G=0.064
Northern Sweden ACPOP Study-wide 600 A=0.950 G=0.050
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 A=0.989 G=0.011
HapMap Global Study-wide 328 A=0.881 G=0.119
HapMap African Sub 120 A=0.950 G=0.050
HapMap American Sub 120 A=0.933 G=0.067
HapMap Asian Sub 88 A=0.72 G=0.28
Qatari Global Study-wide 216 A=0.917 G=0.083
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.858 G=0.142
SGDP_PRJ Global Study-wide 150 A=0.387 G=0.613
The Danish reference pan genome Danish Study-wide 40 A=0.88 G=0.12
Siberian Global Study-wide 16 A=0.50 G=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 12 NC_000012.12:g.113273459A>G
GRCh37.p13 chr 12 NC_000012.11:g.113711264A>G
Gene: TPCN1, two pore segment channel 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TPCN1 transcript variant 1 NM_001143819.3:c.1059-110…

NM_001143819.3:c.1059-110A>G

N/A Intron Variant
TPCN1 transcript variant 3 NM_001301214.2:c.639-110A…

NM_001301214.2:c.639-110A>G

N/A Intron Variant
TPCN1 transcript variant 4 NM_001351346.2:c.639-110A…

NM_001351346.2:c.639-110A>G

N/A Intron Variant
TPCN1 transcript variant 5 NM_001351347.1:c.639-110A…

NM_001351347.1:c.639-110A>G

N/A Intron Variant
TPCN1 transcript variant 2 NM_017901.6:c.843-110A>G N/A Intron Variant
TPCN1 transcript variant X2 XM_011538492.3:c.843-110A…

XM_011538492.3:c.843-110A>G

N/A Intron Variant
TPCN1 transcript variant X5 XM_011538493.3:c.639-110A…

XM_011538493.3:c.639-110A>G

N/A Intron Variant
TPCN1 transcript variant X1 XM_017019480.3:c.1059-110…

XM_017019480.3:c.1059-110A>G

N/A Intron Variant
TPCN1 transcript variant X3 XM_047429011.1:c.843-110A…

XM_047429011.1:c.843-110A>G

N/A Intron Variant
TPCN1 transcript variant X4 XM_047429012.1:c.765-110A…

XM_047429012.1:c.765-110A>G

N/A Intron Variant
TPCN1 transcript variant X6 XM_047429013.1:c.639-110A…

XM_047429013.1:c.639-110A>G

N/A Intron Variant
TPCN1 transcript variant X7 XM_047429014.1:c.639-110A…

XM_047429014.1:c.639-110A>G

N/A Intron Variant
TPCN1 transcript variant X8 XM_047429015.1:c.639-110A…

XM_047429015.1:c.639-110A>G

N/A Intron Variant
TPCN1 transcript variant X10 XM_047429016.1:c.843-110A…

XM_047429016.1:c.843-110A>G

N/A Intron Variant
TPCN1 transcript variant X9 XR_001748766.3:n. 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 12 NC_000012.12:g.113273459= NC_000012.12:g.113273459A>G
GRCh37.p13 chr 12 NC_000012.11:g.113711264= NC_000012.11:g.113711264A>G
TPCN1 transcript variant 1 NM_001143819.1:c.1059-110= NM_001143819.1:c.1059-110A>G
TPCN1 transcript variant 1 NM_001143819.3:c.1059-110= NM_001143819.3:c.1059-110A>G
TPCN1 transcript variant 3 NM_001301214.2:c.639-110= NM_001301214.2:c.639-110A>G
TPCN1 transcript variant 4 NM_001351346.2:c.639-110= NM_001351346.2:c.639-110A>G
TPCN1 transcript variant 5 NM_001351347.1:c.639-110= NM_001351347.1:c.639-110A>G
TPCN1 transcript variant 2 NM_017901.4:c.843-110= NM_017901.4:c.843-110A>G
TPCN1 transcript variant 2 NM_017901.6:c.843-110= NM_017901.6:c.843-110A>G
TPCN1 transcript variant X1 XM_005253904.1:c.1059-110= XM_005253904.1:c.1059-110A>G
TPCN1 transcript variant X2 XM_005253905.1:c.1059-110= XM_005253905.1:c.1059-110A>G
TPCN1 transcript variant X3 XM_005253906.1:c.639-110= XM_005253906.1:c.639-110A>G
TPCN1 transcript variant X2 XM_011538492.3:c.843-110= XM_011538492.3:c.843-110A>G
TPCN1 transcript variant X5 XM_011538493.3:c.639-110= XM_011538493.3:c.639-110A>G
TPCN1 transcript variant X1 XM_017019480.3:c.1059-110= XM_017019480.3:c.1059-110A>G
TPCN1 transcript variant X3 XM_047429011.1:c.843-110= XM_047429011.1:c.843-110A>G
TPCN1 transcript variant X4 XM_047429012.1:c.765-110= XM_047429012.1:c.765-110A>G
TPCN1 transcript variant X6 XM_047429013.1:c.639-110= XM_047429013.1:c.639-110A>G
TPCN1 transcript variant X7 XM_047429014.1:c.639-110= XM_047429014.1:c.639-110A>G
TPCN1 transcript variant X8 XM_047429015.1:c.639-110= XM_047429015.1:c.639-110A>G
TPCN1 transcript variant X10 XM_047429016.1:c.843-110= XM_047429016.1:c.843-110A>G
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#.

68 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss3250264 Sep 28, 2001 (100)
2 BCM_SSAHASNP ss11047961 Jul 11, 2003 (116)
3 WI_SSAHASNP ss12220233 Jul 11, 2003 (116)
4 PERLEGEN ss23952557 Sep 20, 2004 (123)
5 HGSV ss78902771 Dec 06, 2007 (129)
6 BCMHGSC_JDW ss89392705 Mar 24, 2008 (129)
7 1000GENOMES ss112448207 Jan 25, 2009 (130)
8 ILLUMINA-UK ss119720851 Dec 01, 2009 (131)
9 ENSEMBL ss133367344 Dec 01, 2009 (131)
10 GMI ss157922830 Dec 01, 2009 (131)
11 BUSHMAN ss198706726 Jul 04, 2010 (132)
12 BCM-HGSC-SUB ss208341463 Jul 04, 2010 (132)
13 1000GENOMES ss225967699 Jul 14, 2010 (132)
14 1000GENOMES ss236092866 Jul 15, 2010 (132)
15 1000GENOMES ss242619318 Jul 15, 2010 (132)
16 GMI ss281552203 May 04, 2012 (137)
17 GMI ss286629155 Apr 25, 2013 (138)
18 PJP ss291342669 May 09, 2011 (134)
19 TISHKOFF ss563413286 Apr 25, 2013 (138)
20 SSMP ss658996402 Apr 25, 2013 (138)
21 EVA-GONL ss989973803 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1078780328 Aug 21, 2014 (142)
23 1000GENOMES ss1346697428 Aug 21, 2014 (142)
24 EVA_GENOME_DK ss1576532870 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1629478377 Apr 01, 2015 (144)
26 EVA_DECODE ss1642080389 Apr 01, 2015 (144)
27 EVA_UK10K_TWINSUK ss1672472410 Apr 01, 2015 (144)
28 EVA_MGP ss1711344127 Apr 01, 2015 (144)
29 WEILL_CORNELL_DGM ss1933326355 Feb 12, 2016 (147)
30 GENOMED ss1967684266 Jul 19, 2016 (147)
31 JJLAB ss2027420168 Sep 14, 2016 (149)
32 USC_VALOUEV ss2155770500 Dec 20, 2016 (150)
33 HUMAN_LONGEVITY ss2193317337 Dec 20, 2016 (150)
34 SYSTEMSBIOZJU ss2628191275 Nov 08, 2017 (151)
35 GRF ss2700128563 Nov 08, 2017 (151)
36 GNOMAD ss2915356549 Nov 08, 2017 (151)
37 SWEGEN ss3010372561 Nov 08, 2017 (151)
38 CSHL ss3350255117 Nov 08, 2017 (151)
39 OMUKHERJEE_ADBS ss3646447635 Oct 12, 2018 (152)
40 EGCUT_WGS ss3677672998 Jul 13, 2019 (153)
41 EVA_DECODE ss3694495392 Jul 13, 2019 (153)
42 ACPOP ss3739393879 Jul 13, 2019 (153)
43 EVA ss3750981926 Jul 13, 2019 (153)
44 PACBIO ss3787339757 Jul 13, 2019 (153)
45 PACBIO ss3792421150 Jul 13, 2019 (153)
46 PACBIO ss3797304243 Jul 13, 2019 (153)
47 KHV_HUMAN_GENOMES ss3816313301 Jul 13, 2019 (153)
48 EVA ss3833332438 Apr 27, 2020 (154)
49 SGDP_PRJ ss3879141982 Apr 27, 2020 (154)
50 KRGDB ss3927891123 Apr 27, 2020 (154)
51 KOGIC ss3972760855 Apr 27, 2020 (154)
52 FSA-LAB ss3984038095 Apr 25, 2021 (155)
53 EVA ss3986587385 Apr 25, 2021 (155)
54 TOPMED ss4933316306 Apr 25, 2021 (155)
55 TOMMO_GENOMICS ss5208235534 Apr 25, 2021 (155)
56 1000G_HIGH_COVERAGE ss5292285172 Oct 16, 2022 (156)
57 EVA ss5408324226 Oct 16, 2022 (156)
58 HUGCELL_USP ss5486882830 Oct 16, 2022 (156)
59 EVA ss5510848262 Oct 16, 2022 (156)
60 1000G_HIGH_COVERAGE ss5590537315 Oct 16, 2022 (156)
61 SANFORD_IMAGENETICS ss5653983834 Oct 16, 2022 (156)
62 TOMMO_GENOMICS ss5758582653 Oct 16, 2022 (156)
63 YY_MCH ss5813657143 Oct 16, 2022 (156)
64 EVA ss5838533834 Oct 16, 2022 (156)
65 EVA ss5848363732 Oct 16, 2022 (156)
66 EVA ss5850552426 Oct 16, 2022 (156)
67 EVA ss5906081634 Oct 16, 2022 (156)
68 EVA ss5945392632 Oct 16, 2022 (156)
69 1000Genomes NC_000012.11 - 113711264 Oct 12, 2018 (152)
70 1000Genomes_30x NC_000012.12 - 113273459 Oct 16, 2022 (156)
71 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 113711264 Oct 12, 2018 (152)
72 Genetic variation in the Estonian population NC_000012.11 - 113711264 Oct 12, 2018 (152)
73 The Danish reference pan genome NC_000012.11 - 113711264 Apr 27, 2020 (154)
74 gnomAD - Genomes NC_000012.12 - 113273459 Apr 25, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000012.11 - 113711264 Apr 27, 2020 (154)
76 HapMap NC_000012.12 - 113273459 Apr 27, 2020 (154)
77 KOREAN population from KRGDB NC_000012.11 - 113711264 Apr 27, 2020 (154)
78 Korean Genome Project NC_000012.12 - 113273459 Apr 27, 2020 (154)
79 Medical Genome Project healthy controls from Spanish population NC_000012.11 - 113711264 Apr 27, 2020 (154)
80 Northern Sweden NC_000012.11 - 113711264 Jul 13, 2019 (153)
81 Qatari NC_000012.11 - 113711264 Apr 27, 2020 (154)
82 SGDP_PRJ NC_000012.11 - 113711264 Apr 27, 2020 (154)
83 Siberian NC_000012.11 - 113711264 Apr 27, 2020 (154)
84 8.3KJPN NC_000012.11 - 113711264 Apr 25, 2021 (155)
85 14KJPN NC_000012.12 - 113273459 Oct 16, 2022 (156)
86 TopMed NC_000012.12 - 113273459 Apr 25, 2021 (155)
87 UK 10K study - Twins NC_000012.11 - 113711264 Oct 12, 2018 (152)
88 A Vietnamese Genetic Variation Database NC_000012.11 - 113711264 Jul 13, 2019 (153)
89 ALFA NC_000012.12 - 113273459 Apr 25, 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
ss78902771 NC_000012.9:112173983:A:G NC_000012.12:113273458:A:G (self)
ss89392705, ss112448207, ss119720851, ss198706726, ss208341463, ss281552203, ss286629155, ss291342669, ss1642080389 NC_000012.10:112195646:A:G NC_000012.12:113273458:A:G (self)
59510280, 33052203, 23411246, 3132181, 14741885, 35068517, 459887, 12678744, 15368285, 31158962, 8286854, 66204841, 33052203, 7332394, ss225967699, ss236092866, ss242619318, ss563413286, ss658996402, ss989973803, ss1078780328, ss1346697428, ss1576532870, ss1629478377, ss1672472410, ss1711344127, ss1933326355, ss1967684266, ss2027420168, ss2155770500, ss2628191275, ss2700128563, ss2915356549, ss3010372561, ss3350255117, ss3646447635, ss3677672998, ss3739393879, ss3750981926, ss3787339757, ss3792421150, ss3797304243, ss3833332438, ss3879141982, ss3927891123, ss3984038095, ss3986587385, ss5208235534, ss5408324226, ss5510848262, ss5653983834, ss5838533834, ss5848363732, ss5945392632 NC_000012.11:113711263:A:G NC_000012.12:113273458:A:G (self)
78063250, 419794293, 907169, 29138856, 92419757, 148861963, 12866217221, ss2193317337, ss3694495392, ss3816313301, ss3972760855, ss4933316306, ss5292285172, ss5486882830, ss5590537315, ss5758582653, ss5813657143, ss5850552426, ss5906081634 NC_000012.12:113273458:A:G NC_000012.12:113273458:A:G (self)
ss11047961, ss12220233 NT_009775.13:2498142:A:G NC_000012.12:113273458:A:G (self)
ss3250264, ss23952557, ss133367344, ss157922830 NT_009775.17:4287793:A:G NC_000012.12:113273458: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 rs2303617

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