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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.

rs802515

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:146246538 (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>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.064729 (17133/264690, TOPMED)
A=0.01646 (465/28258, 14KJPN)
A=0.01814 (304/16758, 8.3KJPN) (+ 9 more)
A=0.0429 (275/6404, 1000G_30x)
A=0.0413 (207/5008, 1000G)
A=0.1195 (543/4544, ALFA)
A=0.1045 (468/4480, Estonian)
A=0.0410 (120/2926, KOREAN)
A=0.077 (77/998, GoNL)
A=0.063 (38/600, NorthernSweden)
A=0.078 (43/554, SGDP_PRJ)
A=0.042 (9/216, Qatari)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CNTNAP2 : 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 4544 A=0.1195 C=0.0000, G=0.8805
European Sub 4518 A=0.1162 C=0.0000, G=0.8838
African Sub 12 A=1.00 C=0.00, G=0.00
African Others Sub 0 A=0 C=0, G=0
African American Sub 12 A=1.00 C=0.00, G=0.00
Asian Sub 0 A=0 C=0, G=0
East Asian Sub 0 A=0 C=0, G=0
Other Asian Sub 0 A=0 C=0, G=0
Latin American 1 Sub 0 A=0 C=0, G=0
Latin American 2 Sub 4 A=1.0 C=0.0, G=0.0
South Asian Sub 0 A=0 C=0, G=0
Other Sub 10 A=0.2 C=0.0, G=0.8


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=0.064729 G=0.935271
14KJPN JAPANESE Study-wide 28258 A=0.01646 G=0.98354
8.3KJPN JAPANESE Study-wide 16758 A=0.01814 G=0.98186
1000Genomes_30x Global Study-wide 6404 A=0.0429 C=0.0067, G=0.9503
1000Genomes_30x African Sub 1786 A=0.0554 C=0.0230, G=0.9216
1000Genomes_30x Europe Sub 1266 A=0.0664 C=0.0000, G=0.9336
1000Genomes_30x South Asian Sub 1202 A=0.0183 C=0.0000, G=0.9817
1000Genomes_30x East Asian Sub 1170 A=0.0231 C=0.0000, G=0.9769
1000Genomes_30x American Sub 980 A=0.044 C=0.002, G=0.954
1000Genomes Global Study-wide 5008 A=0.0413 C=0.0058, G=0.9529
1000Genomes African Sub 1322 A=0.0605 C=0.0212, G=0.9183
1000Genomes East Asian Sub 1008 A=0.0169 C=0.0000, G=0.9831
1000Genomes Europe Sub 1006 A=0.0676 C=0.0000, G=0.9324
1000Genomes South Asian Sub 978 A=0.015 C=0.000, G=0.985
1000Genomes American Sub 694 A=0.039 C=0.001, G=0.960
Allele Frequency Aggregator Total Global 4544 A=0.1195 C=0.0000, G=0.8805
Allele Frequency Aggregator European Sub 4518 A=0.1162 C=0.0000, G=0.8838
Allele Frequency Aggregator African Sub 12 A=1.00 C=0.00, G=0.00
Allele Frequency Aggregator Other Sub 10 A=0.2 C=0.0, G=0.8
Allele Frequency Aggregator Latin American 2 Sub 4 A=1.0 C=0.0, G=0.0
Allele Frequency Aggregator Latin American 1 Sub 0 A=0 C=0, G=0
Allele Frequency Aggregator South Asian Sub 0 A=0 C=0, G=0
Allele Frequency Aggregator Asian Sub 0 A=0 C=0, G=0
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.1045 G=0.8955
KOREAN population from KRGDB KOREAN Study-wide 2926 A=0.0410 C=0.0000, G=0.9590, T=0.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.077 G=0.923
Northern Sweden ACPOP Study-wide 600 A=0.063 G=0.937
SGDP_PRJ Global Study-wide 554 A=0.078 G=0.922
Qatari Global Study-wide 216 A=0.042 G=0.958
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 7 NC_000007.14:g.146246538A>C
GRCh38.p14 chr 7 NC_000007.14:g.146246538A>G
GRCh38.p14 chr 7 NC_000007.14:g.146246538A>T
GRCh37.p13 chr 7 NC_000007.13:g.145943630A>C
GRCh37.p13 chr 7 NC_000007.13:g.145943630A>G
GRCh37.p13 chr 7 NC_000007.13:g.145943630A>T
CNTNAP2 RefSeqGene NG_007092.3:g.135538A>C
CNTNAP2 RefSeqGene NG_007092.3:g.135538A>G
CNTNAP2 RefSeqGene NG_007092.3:g.135538A>T
Gene: CNTNAP2, contactin associated protein 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CNTNAP2 transcript NM_014141.6:c.97+129565A>C N/A Intron Variant
CNTNAP2 transcript variant X1 XM_017011950.3:c.97+12956…

XM_017011950.3:c.97+129565A>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= C G T
GRCh38.p14 chr 7 NC_000007.14:g.146246538= NC_000007.14:g.146246538A>C NC_000007.14:g.146246538A>G NC_000007.14:g.146246538A>T
GRCh37.p13 chr 7 NC_000007.13:g.145943630= NC_000007.13:g.145943630A>C NC_000007.13:g.145943630A>G NC_000007.13:g.145943630A>T
CNTNAP2 RefSeqGene NG_007092.3:g.135538= NG_007092.3:g.135538A>C NG_007092.3:g.135538A>G NG_007092.3:g.135538A>T
CNTNAP2 transcript NM_014141.5:c.97+129565= NM_014141.5:c.97+129565A>C NM_014141.5:c.97+129565A>G NM_014141.5:c.97+129565A>T
CNTNAP2 transcript NM_014141.6:c.97+129565= NM_014141.6:c.97+129565A>C NM_014141.6:c.97+129565A>G NM_014141.6:c.97+129565A>T
CNTNAP2 transcript variant X1 XM_017011950.3:c.97+129565= XM_017011950.3:c.97+129565A>C XM_017011950.3:c.97+129565A>G XM_017011950.3:c.97+129565A>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#.

45 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss1015755 Oct 05, 2000 (86)
2 KWOK ss1966227 Oct 18, 2000 (87)
3 WUGSC_SSAHASNP ss14537495 Dec 05, 2003 (126)
4 SSAHASNP ss22517015 Apr 05, 2004 (121)
5 SSAHASNP ss22888179 Apr 05, 2004 (121)
6 HGSV ss78194118 Dec 06, 2007 (129)
7 BCMHGSC_JDW ss93784110 Mar 25, 2008 (129)
8 BUSHMAN ss198438915 Jul 04, 2010 (142)
9 BCM-HGSC-SUB ss208457474 Jul 04, 2010 (142)
10 GMI ss279574106 May 04, 2012 (137)
11 1000GENOMES ss460057912 Sep 17, 2011 (135)
12 EVA-GONL ss984919361 Aug 21, 2014 (142)
13 1000GENOMES ss1327596255 Aug 21, 2014 (142)
14 1000GENOMES ss1327596256 Aug 21, 2014 (142)
15 DDI ss1431315268 Apr 01, 2015 (144)
16 HAMMER_LAB ss1805274797 Sep 08, 2015 (146)
17 WEILL_CORNELL_DGM ss1928177651 Feb 12, 2016 (147)
18 GRF ss2708727120 Nov 08, 2017 (151)
19 GNOMAD ss2860444427 Nov 08, 2017 (151)
20 SWEGEN ss3002234570 Nov 08, 2017 (151)
21 CSHL ss3347898676 Nov 08, 2017 (151)
22 URBANLAB ss3648780231 Oct 12, 2018 (152)
23 EGCUT_WGS ss3669979048 Jul 13, 2019 (153)
24 ACPOP ss3735171021 Jul 13, 2019 (153)
25 EVA ss3767300459 Jul 13, 2019 (153)
26 PACBIO ss3785991007 Jul 13, 2019 (153)
27 PACBIO ss3791264308 Jul 13, 2019 (153)
28 PACBIO ss3796144573 Jul 13, 2019 (153)
29 EVA ss3830878612 Apr 26, 2020 (154)
30 EVA ss3838938632 Apr 26, 2020 (154)
31 EVA ss3844395947 Apr 26, 2020 (154)
32 SGDP_PRJ ss3868642386 Apr 26, 2020 (154)
33 KRGDB ss3916030341 Apr 26, 2020 (154)
34 TOPMED ss4767784008 Apr 26, 2021 (155)
35 TOMMO_GENOMICS ss5186117317 Apr 26, 2021 (155)
36 1000G_HIGH_COVERAGE ss5275155036 Oct 13, 2022 (156)
37 1000G_HIGH_COVERAGE ss5275155037 Oct 13, 2022 (156)
38 HUGCELL_USP ss5471989062 Oct 13, 2022 (156)
39 HUGCELL_USP ss5471989063 Oct 13, 2022 (156)
40 1000G_HIGH_COVERAGE ss5564523716 Oct 13, 2022 (156)
41 SANFORD_IMAGENETICS ss5644220446 Oct 13, 2022 (156)
42 TOMMO_GENOMICS ss5727286075 Oct 13, 2022 (156)
43 YY_MCH ss5809198757 Oct 13, 2022 (156)
44 EVA ss5823682378 Oct 13, 2022 (156)
45 EVA ss5973424352 Oct 13, 2022 (156)
46 1000Genomes NC_000007.13 - 145943630 Oct 12, 2018 (152)
47 1000Genomes_30x NC_000007.14 - 146246538 Oct 13, 2022 (156)
48 Genetic variation in the Estonian population NC_000007.13 - 145943630 Oct 12, 2018 (152)
49 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 280065559 (NC_000007.14:146246537:A:C 800/137246)
Row 280065560 (NC_000007.14:146246537:A:G 126663/137080)

- Apr 26, 2021 (155)
50 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 280065559 (NC_000007.14:146246537:A:C 800/137246)
Row 280065560 (NC_000007.14:146246537:A:G 126663/137080)

- Apr 26, 2021 (155)
51 Genome of the Netherlands Release 5 NC_000007.13 - 145943630 Apr 26, 2020 (154)
52 KOREAN population from KRGDB NC_000007.13 - 145943630 Apr 26, 2020 (154)
53 Northern Sweden NC_000007.13 - 145943630 Jul 13, 2019 (153)
54 Qatari NC_000007.13 - 145943630 Apr 26, 2020 (154)
55 SGDP_PRJ NC_000007.13 - 145943630 Apr 26, 2020 (154)
56 8.3KJPN NC_000007.13 - 145943630 Apr 26, 2021 (155)
57 14KJPN NC_000007.14 - 146246538 Oct 13, 2022 (156)
58 TopMed NC_000007.14 - 146246538 Apr 26, 2021 (155)
59 ALFA NC_000007.14 - 146246538 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)
rs10332347 Mar 11, 2006 (126)
rs17397633 Mar 11, 2006 (126)
rs111696926 Aug 21, 2014 (142)
rs112865151 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
39657162, 23207735, ss1327596255, ss2860444427, ss3916030341, ss5644220446 NC_000007.13:145943629:A:C NC_000007.14:146246537:A:C (self)
52049651, 5334846661, ss5275155037, ss5471989063, ss5564523716 NC_000007.14:146246537:A:C NC_000007.14:146246537:A:C (self)
ss78194118 NC_000007.11:145381277:A:G NC_000007.14:146246537:A:G (self)
ss93784110, ss198438915, ss208457474, ss279574106 NC_000007.12:145574562:A:G NC_000007.14:146246537:A:G (self)
39657162, 15717296, 9846531, 23207735, 8455886, 10219581, 20659366, 44086624, ss460057912, ss984919361, ss1327596256, ss1431315268, ss1805274797, ss1928177651, ss2708727120, ss2860444427, ss3002234570, ss3347898676, ss3669979048, ss3735171021, ss3767300459, ss3785991007, ss3791264308, ss3796144573, ss3830878612, ss3838938632, ss3868642386, ss3916030341, ss5186117317, ss5644220446, ss5823682378, ss5973424352 NC_000007.13:145943629:A:G NC_000007.14:146246537:A:G (self)
52049651, 61123179, 605161567, 5334846661, ss3648780231, ss3844395947, ss4767784008, ss5275155036, ss5471989062, ss5564523716, ss5727286075, ss5809198757 NC_000007.14:146246537:A:G NC_000007.14:146246537:A:G (self)
ss14537495, ss22517015, ss22888179 NT_007914.13:6519645:A:G NC_000007.14:146246537:A:G (self)
ss1015755, ss1966227 NT_007914.15:6539252:A:G NC_000007.14:146246537:A:G (self)
23207735, ss3916030341 NC_000007.13:145943629:A:T NC_000007.14:146246537:A: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 rs802515

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