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dbSNP Short Genetic Variations

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.

rs12995399

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr2:222272282 (GRCh38.p12) 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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.21544 (27052/125568, TOPMED)
C=0.2016 (6240/30948, GnomAD)
C=0.264 (1324/5008, 1000G) (+ 3 more)
C=0.197 (884/4480, Estonian)
C=0.225 (867/3854, ALSPAC)
C=0.227 (843/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PAX3 : Intron Variant
Publications
1 citation
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.p12 chr 2 NC_000002.12:g.222272282T>C
GRCh37.p13 chr 2 NC_000002.11:g.223137001T>C
PAX3 RefSeqGene NG_011632.1:g.31700A>G
Gene: PAX3, paired box 3 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PAX3 transcript variant PAX3I NM_001127366.2:c. N/A Intron Variant
PAX3 transcript variant PAX3 NM_181457.3:c. N/A Intron Variant
PAX3 transcript variant PAX3D NM_181458.3:c. N/A Intron Variant
PAX3 transcript variant PAX3E NM_181459.3:c. N/A Intron Variant
PAX3 transcript variant PAX3H NM_181460.3:c. N/A Intron Variant
PAX3 transcript variant PAX3G NM_181461.3:c. N/A Intron Variant
PAX3 transcript variant PAX3A NM_000438.5:c. N/A Genic Downstream Transcript Variant
PAX3 transcript variant PAX3B NM_013942.4:c. N/A Genic Downstream Transcript 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

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 125568 T=0.78456 C=0.21544
gnomAD - Genomes Global Study-wide 30948 T=0.7984 C=0.2016
gnomAD - Genomes European Sub 18486 T=0.7917 C=0.2083
gnomAD - Genomes African Sub 8722 T=0.860 C=0.140
gnomAD - Genomes East Asian Sub 1618 T=0.676 C=0.324
gnomAD - Genomes Other Sub 982 T=0.77 C=0.23
gnomAD - Genomes American Sub 838 T=0.56 C=0.44
gnomAD - Genomes Ashkenazi Jewish Sub 302 T=0.80 C=0.20
1000Genomes Global Study-wide 5008 T=0.736 C=0.264
1000Genomes African Sub 1322 T=0.889 C=0.111
1000Genomes East Asian Sub 1008 T=0.629 C=0.371
1000Genomes Europe Sub 1006 T=0.798 C=0.202
1000Genomes South Asian Sub 978 T=0.67 C=0.33
1000Genomes American Sub 694 T=0.60 C=0.40
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.803 C=0.197
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.775 C=0.225
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.773 C=0.227
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 T= C Note
GRCh38.p12 chr 2 NC_000002.12:g.222272282T= NC_000002.12:g.22227228...

NC_000002.12:g.222272282T>C

GRCh37.p13 chr 2 NC_000002.11:g.223137001T= NC_000002.11:g.22313700...

NC_000002.11:g.223137001T>C

PAX3 RefSeqGene NG_011632.1:g.31700A= NG_011632.1:g.31700A>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#.

84 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 SSAHASNP ss21593378 Apr 05, 2004 (121)
2 PERLEGEN ss23918920 Sep 20, 2004 (123)
3 ABI ss44362539 Mar 15, 2006 (126)
4 ILLUMINA ss67051232 Nov 30, 2006 (127)
5 ILLUMINA ss67377462 Nov 30, 2006 (127)
6 ILLUMINA ss68142822 Dec 12, 2006 (127)
7 EGP_SNPS ss70445665 May 17, 2007 (127)
8 ILLUMINA ss70590936 May 26, 2008 (130)
9 ILLUMINA ss71134598 May 17, 2007 (127)
10 ILLUMINA ss75907595 Dec 07, 2007 (129)
11 KRIBB_YJKIM ss85291640 Dec 16, 2007 (130)
12 BCMHGSC_JDW ss91560724 Mar 24, 2008 (129)
13 HUMANGENOME_JCVI ss96475220 Feb 06, 2009 (130)
14 BGI ss106163834 Feb 06, 2009 (130)
15 ENSEMBL ss135957593 Dec 01, 2009 (131)
16 ILLUMINA ss153306091 Dec 01, 2009 (131)
17 ILLUMINA ss159241482 Dec 01, 2009 (131)
18 ILLUMINA ss160311434 Dec 01, 2009 (131)
19 ILLUMINA ss172298992 Jul 04, 2010 (132)
20 1000GENOMES ss219834820 Jul 14, 2010 (132)
21 1000GENOMES ss231601701 Jul 14, 2010 (132)
22 1000GENOMES ss239057316 Jul 15, 2010 (132)
23 BL ss253895628 May 09, 2011 (134)
24 GMI ss276912582 May 04, 2012 (137)
25 GMI ss284548571 Apr 25, 2013 (138)
26 PJP ss292495302 May 09, 2011 (134)
27 ILLUMINA ss479854600 May 04, 2012 (137)
28 ILLUMINA ss479862210 May 04, 2012 (137)
29 ILLUMINA ss480462391 Sep 08, 2015 (146)
30 ILLUMINA ss484725816 May 04, 2012 (137)
31 ILLUMINA ss536826665 Sep 08, 2015 (146)
32 TISHKOFF ss556247868 Apr 25, 2013 (138)
33 SSMP ss649911183 Apr 25, 2013 (138)
34 ILLUMINA ss778793911 Sep 08, 2015 (146)
35 ILLUMINA ss782809606 Sep 08, 2015 (146)
36 ILLUMINA ss783774877 Sep 08, 2015 (146)
37 ILLUMINA ss832062762 Sep 08, 2015 (146)
38 ILLUMINA ss834253994 Sep 08, 2015 (146)
39 EVA-GONL ss978000948 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1069971019 Aug 21, 2014 (142)
41 1000GENOMES ss1301803260 Aug 21, 2014 (142)
42 EVA_GENOME_DK ss1579338830 Apr 01, 2015 (144)
43 EVA_DECODE ss1587457242 Apr 01, 2015 (144)
44 EVA_UK10K_ALSPAC ss1605878963 Apr 01, 2015 (144)
45 EVA_UK10K_TWINSUK ss1648872996 Apr 01, 2015 (144)
46 EVA_SVP ss1712533921 Apr 01, 2015 (144)
47 ILLUMINA ss1752341045 Sep 08, 2015 (146)
48 WEILL_CORNELL_DGM ss1921246315 Feb 12, 2016 (147)
49 ILLUMINA ss1946067753 Feb 12, 2016 (147)
50 ILLUMINA ss1958509249 Feb 12, 2016 (147)
51 GENOMED ss1969035249 Jul 19, 2016 (147)
52 JJLAB ss2021171349 Sep 14, 2016 (149)
53 USC_VALOUEV ss2149234581 Dec 20, 2016 (150)
54 HUMAN_LONGEVITY ss2239482589 Dec 20, 2016 (150)
55 TOPMED ss2405940087 Dec 20, 2016 (150)
56 SYSTEMSBIOZJU ss2625085840 Nov 08, 2017 (151)
57 ILLUMINA ss2633744907 Nov 08, 2017 (151)
58 GRF ss2703884234 Nov 08, 2017 (151)
59 GNOMAD ss2786775851 Nov 08, 2017 (151)
60 SWEGEN ss2991421253 Nov 08, 2017 (151)
61 ILLUMINA ss3022073823 Nov 08, 2017 (151)
62 BIOINF_KMB_FNS_UNIBA ss3024344044 Nov 08, 2017 (151)
63 TOPMED ss3339428395 Nov 08, 2017 (151)
64 CSHL ss3344758798 Nov 08, 2017 (151)
65 ILLUMINA ss3625777382 Oct 11, 2018 (152)
66 ILLUMINA ss3628295941 Oct 11, 2018 (152)
67 ILLUMINA ss3631704594 Oct 11, 2018 (152)
68 ILLUMINA ss3633235786 Oct 11, 2018 (152)
69 ILLUMINA ss3633949034 Oct 11, 2018 (152)
70 ILLUMINA ss3634814339 Oct 11, 2018 (152)
71 ILLUMINA ss3635634440 Oct 11, 2018 (152)
72 ILLUMINA ss3636504144 Oct 11, 2018 (152)
73 ILLUMINA ss3637386468 Oct 11, 2018 (152)
74 ILLUMINA ss3638321128 Oct 11, 2018 (152)
75 ILLUMINA ss3639163823 Oct 11, 2018 (152)
76 ILLUMINA ss3639885936 Oct 11, 2018 (152)
77 ILLUMINA ss3640521638 Oct 11, 2018 (152)
78 ILLUMINA ss3641121297 Oct 11, 2018 (152)
79 ILLUMINA ss3641417422 Oct 11, 2018 (152)
80 ILLUMINA ss3643285585 Oct 11, 2018 (152)
81 ILLUMINA ss3643933856 Oct 11, 2018 (152)
82 ILLUMINA ss3644770427 Oct 11, 2018 (152)
83 URBANLAB ss3647283984 Oct 11, 2018 (152)
84 ILLUMINA ss3652525172 Oct 11, 2018 (152)
85 1000Genomes NC_000002.11 - 223137001 Oct 11, 2018 (152)
86 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 223137001 Oct 11, 2018 (152)
87 Genetic variation in the Estonian population NC_000002.11 - 223137001 Oct 11, 2018 (152)
88 gnomAD - Genomes NC_000002.11 - 223137001 Oct 11, 2018 (152)
89 TopMed NC_000002.12 - 222272282 Oct 11, 2018 (152)
90 UK 10K study - Twins NC_000002.11 - 223137001 Oct 11, 2018 (152)
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)
rs61467235 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3639163823, ss3639885936, ss3643933856 NC_000002.9:222962505:T= NC_000002.12:222272281:T=
ss91560724, ss253895628, ss276912582, ss284548571, ss292495302, ss479854600, ss1587457242, ss1712533921, ss3643285585 NC_000002.10:222845244:T= NC_000002.12:222272281:T= (self)
12914141, 7145530, 5056677, 116265712, 7145530, ss219834820, ss231601701, ss239057316, ss479862210, ss480462391, ss484725816, ss536826665, ss556247868, ss649911183, ss778793911, ss782809606, ss783774877, ss832062762, ss834253994, ss978000948, ss1069971019, ss1301803260, ss1579338830, ss1605878963, ss1648872996, ss1752341045, ss1921246315, ss1946067753, ss1958509249, ss1969035249, ss2021171349, ss2149234581, ss2405940087, ss2625085840, ss2633744907, ss2703884234, ss2786775851, ss2991421253, ss3022073823, ss3344758798, ss3625777382, ss3628295941, ss3631704594, ss3633235786, ss3633949034, ss3634814339, ss3635634440, ss3636504144, ss3637386468, ss3638321128, ss3640521638, ss3641121297, ss3641417422, ss3644770427, ss3652525172 NC_000002.11:223137000:T= NC_000002.12:222272281:T= (self)
218380712, ss2239482589, ss3024344044, ss3339428395, ss3647283984 NC_000002.12:222272281:T= NC_000002.12:222272281:T= (self)
ss21593378 NT_005403.14:73346412:T= NC_000002.12:222272281:T= (self)
ss23918920, ss44362539, ss67051232, ss67377462, ss68142822, ss70445665, ss70590936, ss71134598, ss75907595, ss85291640, ss96475220, ss106163834, ss135957593, ss153306091, ss159241482, ss160311434, ss172298992 NT_005403.17:73346418:T= NC_000002.12:222272281:T= (self)
ss3639163823, ss3639885936, ss3643933856 NC_000002.9:222962505:T>C NC_000002.12:222272281:T>C
ss91560724, ss253895628, ss276912582, ss284548571, ss292495302, ss479854600, ss1587457242, ss1712533921, ss3643285585 NC_000002.10:222845244:T>C NC_000002.12:222272281:T>C (self)
12914141, 7145530, 5056677, 116265712, 7145530, ss219834820, ss231601701, ss239057316, ss479862210, ss480462391, ss484725816, ss536826665, ss556247868, ss649911183, ss778793911, ss782809606, ss783774877, ss832062762, ss834253994, ss978000948, ss1069971019, ss1301803260, ss1579338830, ss1605878963, ss1648872996, ss1752341045, ss1921246315, ss1946067753, ss1958509249, ss1969035249, ss2021171349, ss2149234581, ss2405940087, ss2625085840, ss2633744907, ss2703884234, ss2786775851, ss2991421253, ss3022073823, ss3344758798, ss3625777382, ss3628295941, ss3631704594, ss3633235786, ss3633949034, ss3634814339, ss3635634440, ss3636504144, ss3637386468, ss3638321128, ss3640521638, ss3641121297, ss3641417422, ss3644770427, ss3652525172 NC_000002.11:223137000:T>C NC_000002.12:222272281:T>C (self)
218380712, ss2239482589, ss3024344044, ss3339428395, ss3647283984 NC_000002.12:222272281:T>C NC_000002.12:222272281:T>C (self)
ss21593378 NT_005403.14:73346412:T>C NC_000002.12:222272281:T>C (self)
ss23918920, ss44362539, ss67051232, ss67377462, ss68142822, ss70445665, ss70590936, ss71134598, ss75907595, ss85291640, ss96475220, ss106163834, ss135957593, ss153306091, ss159241482, ss160311434, ss172298992 NT_005403.17:73346418:T>C NC_000002.12:222272281:T>C (self)
Help

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

1 citation for rs12995399
PMID Title Author Year Journal
23751107 Evaluation of PAX3 genetic variants and nevus number. Ogbah Z et al. 2013 Pigment cell & melanoma research

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.post58+e54ea20