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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs417

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:91951807 (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
C>A / C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.454177 (120216/264690, TOPMED)
C=0.455784 (63797/139972, GnomAD)
C=0.41182 (24654/59866, ALFA) (+ 17 more)
C=0.21346 (6032/28258, 14KJPN)
C=0.21381 (3583/16758, 8.3KJPN)
C=0.4297 (2752/6404, 1000G_30x)
C=0.4223 (2115/5008, 1000G)
C=0.3694 (1655/4480, Estonian)
C=0.3923 (1512/3854, ALSPAC)
C=0.3784 (1403/3708, TWINSUK)
C=0.2177 (638/2930, KOREAN)
C=0.4475 (844/1886, HapMap)
C=0.1861 (341/1832, Korea1K)
C=0.363 (362/998, GoNL)
C=0.448 (269/600, NorthernSweden)
C=0.248 (119/480, SGDP_PRJ)
C=0.454 (98/216, Qatari)
C=0.215 (46/214, Vietnamese)
C=0.25 (11/44, Siberian)
C=0.33 (13/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AKAP9 : 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 59866 C=0.41182 A=0.58818
European Sub 49142 C=0.38946 A=0.61054
African Sub 5728 C=0.6205 A=0.3795
African Others Sub 206 C=0.660 A=0.340
African American Sub 5522 C=0.6190 A=0.3810
Asian Sub 158 C=0.241 A=0.759
East Asian Sub 124 C=0.242 A=0.758
Other Asian Sub 34 C=0.24 A=0.76
Latin American 1 Sub 492 C=0.407 A=0.593
Latin American 2 Sub 720 C=0.331 A=0.669
South Asian Sub 144 C=0.361 A=0.639
Other Sub 3482 C=0.4115 A=0.5885


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=0.454177 A=0.545823
gnomAD - Genomes Global Study-wide 139972 C=0.455784 A=0.544216
gnomAD - Genomes European Sub 75816 C=0.38393 A=0.61607
gnomAD - Genomes African Sub 41918 C=0.62501 A=0.37499
gnomAD - Genomes American Sub 13638 C=0.37505 A=0.62495
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.5500 A=0.4500
gnomAD - Genomes East Asian Sub 3130 C=0.1927 A=0.8073
gnomAD - Genomes Other Sub 2150 C=0.4400 A=0.5600
Allele Frequency Aggregator Total Global 59866 C=0.41182 A=0.58818
Allele Frequency Aggregator European Sub 49142 C=0.38946 A=0.61054
Allele Frequency Aggregator African Sub 5728 C=0.6205 A=0.3795
Allele Frequency Aggregator Other Sub 3482 C=0.4115 A=0.5885
Allele Frequency Aggregator Latin American 2 Sub 720 C=0.331 A=0.669
Allele Frequency Aggregator Latin American 1 Sub 492 C=0.407 A=0.593
Allele Frequency Aggregator Asian Sub 158 C=0.241 A=0.759
Allele Frequency Aggregator South Asian Sub 144 C=0.361 A=0.639
14KJPN JAPANESE Study-wide 28258 C=0.21346 A=0.78654
8.3KJPN JAPANESE Study-wide 16758 C=0.21381 A=0.78619
1000Genomes_30x Global Study-wide 6404 C=0.4297 A=0.5703
1000Genomes_30x African Sub 1786 C=0.6663 A=0.3337
1000Genomes_30x Europe Sub 1266 C=0.3847 A=0.6153
1000Genomes_30x South Asian Sub 1202 C=0.4185 A=0.5815
1000Genomes_30x East Asian Sub 1170 C=0.1786 A=0.8214
1000Genomes_30x American Sub 980 C=0.370 A=0.630
1000Genomes Global Study-wide 5008 C=0.4223 A=0.5777
1000Genomes African Sub 1322 C=0.6573 A=0.3427
1000Genomes East Asian Sub 1008 C=0.1825 A=0.8175
1000Genomes Europe Sub 1006 C=0.3867 A=0.6133
1000Genomes South Asian Sub 978 C=0.426 A=0.574
1000Genomes American Sub 694 C=0.369 A=0.631
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.3694 A=0.6306
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.3923 A=0.6077
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.3784 A=0.6216
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.2177 A=0.7823, G=0.0000, T=0.0000
HapMap Global Study-wide 1886 C=0.4475 A=0.5525
HapMap American Sub 766 C=0.388 A=0.612
HapMap African Sub 690 C=0.622 A=0.378
HapMap Asian Sub 254 C=0.173 A=0.827
HapMap Europe Sub 176 C=0.420 A=0.580
Korean Genome Project KOREAN Study-wide 1832 C=0.1861 A=0.8139
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.363 A=0.637
Northern Sweden ACPOP Study-wide 600 C=0.448 A=0.552
SGDP_PRJ Global Study-wide 480 C=0.248 A=0.752
Qatari Global Study-wide 216 C=0.454 A=0.546
A Vietnamese Genetic Variation Database Global Study-wide 214 C=0.215 A=0.785
Siberian Global Study-wide 44 C=0.25 A=0.75
The Danish reference pan genome Danish Study-wide 40 C=0.33 A=0.68
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.91951807C>A
GRCh38.p14 chr 7 NC_000007.14:g.91951807C>G
GRCh38.p14 chr 7 NC_000007.14:g.91951807C>T
GRCh37.p13 chr 7 NC_000007.13:g.91581121C>A
GRCh37.p13 chr 7 NC_000007.13:g.91581121C>G
GRCh37.p13 chr 7 NC_000007.13:g.91581121C>T
AKAP9 RefSeqGene (LRG_331) NG_011623.1:g.15933C>A
AKAP9 RefSeqGene (LRG_331) NG_011623.1:g.15933C>G
AKAP9 RefSeqGene (LRG_331) NG_011623.1:g.15933C>T
Gene: AKAP9, A-kinase anchoring protein 9 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
AKAP9 transcript variant 2 NM_005751.5:c.48+10660C>A N/A Intron Variant
AKAP9 transcript variant 3 NM_147185.3:c.48+10660C>A N/A Intron Variant
AKAP9 transcript variant 6 NM_001379277.1:c. N/A Genic Upstream 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

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.p14 chr 7 NC_000007.14:g.91951807= NC_000007.14:g.91951807C>A NC_000007.14:g.91951807C>G NC_000007.14:g.91951807C>T
GRCh37.p13 chr 7 NC_000007.13:g.91581121= NC_000007.13:g.91581121C>A NC_000007.13:g.91581121C>G NC_000007.13:g.91581121C>T
AKAP9 RefSeqGene (LRG_331) NG_011623.1:g.15933= NG_011623.1:g.15933C>A NG_011623.1:g.15933C>G NG_011623.1:g.15933C>T
AKAP9 transcript variant 2 NM_005751.4:c.48+10660= NM_005751.4:c.48+10660C>A NM_005751.4:c.48+10660C>G NM_005751.4:c.48+10660C>T
AKAP9 transcript variant 2 NM_005751.5:c.48+10660= NM_005751.5:c.48+10660C>A NM_005751.5:c.48+10660C>G NM_005751.5:c.48+10660C>T
AKAP9 transcript variant 3 NM_147185.2:c.48+10660= NM_147185.2:c.48+10660C>A NM_147185.2:c.48+10660C>G NM_147185.2:c.48+10660C>T
AKAP9 transcript variant 3 NM_147185.3:c.48+10660= NM_147185.3:c.48+10660C>A NM_147185.3:c.48+10660C>G NM_147185.3:c.48+10660C>T
AKAP9 transcript variant X1 XM_005250102.1:c.48+10660= XM_005250102.1:c.48+10660C>A XM_005250102.1:c.48+10660C>G XM_005250102.1:c.48+10660C>T
AKAP9 transcript variant X2 XM_005250103.1:c.48+10660= XM_005250103.1:c.48+10660C>A XM_005250103.1:c.48+10660C>G XM_005250103.1:c.48+10660C>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#.

85 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss420 Sep 19, 2000 (36)
2 YUSUKE ss3222209 Sep 28, 2001 (100)
3 CSHL-HAPMAP ss17192235 Feb 27, 2004 (120)
4 ABI ss42946926 Mar 13, 2006 (126)
5 ILLUMINA ss75127849 Dec 05, 2007 (129)
6 BGI ss105557396 Feb 06, 2009 (130)
7 1000GENOMES ss112352277 Jan 25, 2009 (130)
8 1000GENOMES ss114094393 Jan 25, 2009 (130)
9 ILLUMINA-UK ss116195152 Dec 01, 2009 (131)
10 KRIBB_YJKIM ss119336852 Dec 01, 2009 (131)
11 GMI ss155192341 Dec 01, 2009 (131)
12 ILLUMINA ss160665368 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss162528893 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss164845256 Jul 04, 2010 (132)
15 ILLUMINA ss173695772 Jul 04, 2010 (132)
16 BUSHMAN ss197907973 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss208308472 Jul 04, 2010 (132)
18 1000GENOMES ss223203768 Jul 14, 2010 (132)
19 1000GENOMES ss234075415 Jul 15, 2010 (132)
20 1000GENOMES ss241011341 Jul 15, 2010 (132)
21 BL ss254516329 May 09, 2011 (134)
22 GMI ss279438212 May 04, 2012 (137)
23 GMI ss285677187 Apr 25, 2013 (138)
24 ILLUMINA ss480901567 May 04, 2012 (137)
25 ILLUMINA ss480920458 May 04, 2012 (137)
26 ILLUMINA ss481876174 Sep 08, 2015 (146)
27 ILLUMINA ss485245764 May 04, 2012 (137)
28 TISHKOFF ss560153054 Apr 25, 2013 (138)
29 SSMP ss654554977 Apr 25, 2013 (138)
30 ILLUMINA ss783068839 Sep 08, 2015 (146)
31 ILLUMINA ss832326928 Sep 08, 2015 (146)
32 EVA-GONL ss984538600 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1074794905 Aug 21, 2014 (142)
34 1000GENOMES ss1326135797 Aug 21, 2014 (142)
35 DDI ss1431208826 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1582306466 Apr 01, 2015 (144)
37 EVA_DECODE ss1594115512 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1618693684 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1661687717 Apr 01, 2015 (144)
40 EVA_SVP ss1712971027 Apr 01, 2015 (144)
41 WEILL_CORNELL_DGM ss1927799986 Feb 12, 2016 (147)
42 JJLAB ss2024583296 Sep 14, 2016 (149)
43 USC_VALOUEV ss2152804195 Dec 20, 2016 (150)
44 HUMAN_LONGEVITY ss2295781355 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2626783594 Nov 08, 2017 (151)
46 GRF ss2708511477 Nov 08, 2017 (151)
47 GNOMAD ss2856168074 Nov 08, 2017 (151)
48 SWEGEN ss3001625998 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3026085262 Nov 08, 2017 (151)
50 CSHL ss3347731028 Nov 08, 2017 (151)
51 ILLUMINA ss3634195615 Oct 12, 2018 (152)
52 ILLUMINA ss3636864015 Oct 12, 2018 (152)
53 ILLUMINA ss3638709987 Oct 12, 2018 (152)
54 ILLUMINA ss3643644968 Oct 12, 2018 (152)
55 URBANLAB ss3648701388 Oct 12, 2018 (152)
56 EGCUT_WGS ss3669381536 Jul 13, 2019 (153)
57 EVA_DECODE ss3720202821 Jul 13, 2019 (153)
58 ACPOP ss3734860223 Jul 13, 2019 (153)
59 EVA ss3766865044 Jul 13, 2019 (153)
60 PACBIO ss3785892409 Jul 13, 2019 (153)
61 PACBIO ss3791183296 Jul 13, 2019 (153)
62 PACBIO ss3796063258 Jul 13, 2019 (153)
63 KHV_HUMAN_GENOMES ss3810038383 Jul 13, 2019 (153)
64 EVA ss3830700151 Apr 26, 2020 (154)
65 EVA ss3838848896 Apr 26, 2020 (154)
66 EVA ss3844303827 Apr 26, 2020 (154)
67 SGDP_PRJ ss3867878964 Apr 26, 2020 (154)
68 KRGDB ss3915148094 Apr 26, 2020 (154)
69 KOGIC ss3962085788 Apr 26, 2020 (154)
70 EVA ss4017347116 Apr 26, 2021 (155)
71 TOPMED ss4754733226 Apr 26, 2021 (155)
72 TOMMO_GENOMICS ss5184424770 Apr 26, 2021 (155)
73 1000G_HIGH_COVERAGE ss5273852565 Oct 16, 2022 (156)
74 EVA ss5375174438 Oct 16, 2022 (156)
75 HUGCELL_USP ss5470840246 Oct 16, 2022 (156)
76 EVA ss5509048682 Oct 16, 2022 (156)
77 1000G_HIGH_COVERAGE ss5562541259 Oct 16, 2022 (156)
78 SANFORD_IMAGENETICS ss5643488555 Oct 16, 2022 (156)
79 TOMMO_GENOMICS ss5725062399 Oct 16, 2022 (156)
80 EVA ss5799730664 Oct 16, 2022 (156)
81 YY_MCH ss5808883017 Oct 16, 2022 (156)
82 EVA ss5823188230 Oct 16, 2022 (156)
83 EVA ss5856002993 Oct 16, 2022 (156)
84 EVA ss5859883093 Oct 16, 2022 (156)
85 EVA ss5972667077 Oct 16, 2022 (156)
86 1000Genomes NC_000007.13 - 91581121 Oct 12, 2018 (152)
87 1000Genomes_30x NC_000007.14 - 91951807 Oct 16, 2022 (156)
88 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 91581121 Oct 12, 2018 (152)
89 Genetic variation in the Estonian population NC_000007.13 - 91581121 Oct 12, 2018 (152)
90 The Danish reference pan genome NC_000007.13 - 91581121 Apr 26, 2020 (154)
91 gnomAD - Genomes NC_000007.14 - 91951807 Apr 26, 2021 (155)
92 Genome of the Netherlands Release 5 NC_000007.13 - 91581121 Apr 26, 2020 (154)
93 HapMap NC_000007.14 - 91951807 Apr 26, 2020 (154)
94 KOREAN population from KRGDB NC_000007.13 - 91581121 Apr 26, 2020 (154)
95 Korean Genome Project NC_000007.14 - 91951807 Apr 26, 2020 (154)
96 Northern Sweden NC_000007.13 - 91581121 Jul 13, 2019 (153)
97 Qatari NC_000007.13 - 91581121 Apr 26, 2020 (154)
98 SGDP_PRJ NC_000007.13 - 91581121 Apr 26, 2020 (154)
99 Siberian NC_000007.13 - 91581121 Apr 26, 2020 (154)
100 8.3KJPN NC_000007.13 - 91581121 Apr 26, 2021 (155)
101 14KJPN NC_000007.14 - 91951807 Oct 16, 2022 (156)
102 TopMed NC_000007.14 - 91951807 Apr 26, 2021 (155)
103 UK 10K study - Twins NC_000007.13 - 91581121 Oct 12, 2018 (152)
104 A Vietnamese Genetic Variation Database NC_000007.13 - 91581121 Jul 13, 2019 (153)
105 ALFA NC_000007.14 - 91951807 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
ss112352277, ss114094393, ss116195152, ss162528893, ss164845256, ss197907973, ss208308472, ss254516329, ss279438212, ss285677187, ss480901567, ss1594115512, ss1712971027, ss3643644968 NC_000007.12:91419056:C:A NC_000007.14:91951806:C:A (self)
38142217, 21224337, 15119784, 8471405, 9476997, 22325488, 8145088, 9841916, 19895944, 5320549, 42394077, 21224337, 4734342, ss223203768, ss234075415, ss241011341, ss480920458, ss481876174, ss485245764, ss560153054, ss654554977, ss783068839, ss832326928, ss984538600, ss1074794905, ss1326135797, ss1431208826, ss1582306466, ss1618693684, ss1661687717, ss1927799986, ss2024583296, ss2152804195, ss2626783594, ss2708511477, ss2856168074, ss3001625998, ss3347731028, ss3634195615, ss3636864015, ss3638709987, ss3669381536, ss3734860223, ss3766865044, ss3785892409, ss3791183296, ss3796063258, ss3830700151, ss3838848896, ss3867878964, ss3915148094, ss4017347116, ss5184424770, ss5375174438, ss5509048682, ss5643488555, ss5799730664, ss5823188230, ss5972667077 NC_000007.13:91581120:C:A NC_000007.14:91951806:C:A (self)
50067194, 269107580, 3446348, 18463789, 58899503, 592110785, 4442794616, ss2295781355, ss3026085262, ss3648701388, ss3720202821, ss3810038383, ss3844303827, ss3962085788, ss4754733226, ss5273852565, ss5470840246, ss5562541259, ss5725062399, ss5808883017, ss5856002993, ss5859883093 NC_000007.14:91951806:C:A NC_000007.14:91951806:C:A (self)
ss17192235 NT_007933.13:16815336:C:A NC_000007.14:91951806:C:A (self)
ss420, ss3222209, ss42946926, ss75127849, ss105557396, ss119336852, ss155192341, ss160665368, ss173695772 NT_007933.15:29613963:C:A NC_000007.14:91951806:C:A (self)
22325488, ss3915148094 NC_000007.13:91581120:C:G NC_000007.14:91951806:C:G (self)
22325488, ss3915148094 NC_000007.13:91581120:C:T NC_000007.14:91951806:C: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 rs417

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