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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.

rs416

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:91951257 (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=0.415214 (109903/264690, TOPMED)
A=0.418420 (58439/139666, GnomAD)
A=0.40451 (13856/34254, ALFA) (+ 16 more)
A=0.19525 (5517/28256, 14KJPN)
A=0.19501 (3268/16758, 8.3KJPN)
A=0.3743 (2397/6404, 1000G_30x)
A=0.3714 (1860/5008, 1000G)
A=0.3692 (1654/4480, Estonian)
A=0.3923 (1512/3854, ALSPAC)
A=0.3784 (1403/3708, TWINSUK)
A=0.1933 (566/2928, KOREAN)
A=0.1599 (293/1832, Korea1K)
A=0.363 (362/998, GoNL)
A=0.448 (269/600, NorthernSweden)
A=0.244 (122/500, SGDP_PRJ)
A=0.435 (94/216, Qatari)
A=0.181 (39/216, Vietnamese)
A=0.26 (11/42, Siberian)
A=0.35 (14/40, 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 34254 A=0.40451 G=0.59549, T=0.00000
European Sub 29792 A=0.39756 G=0.60244, T=0.00000
African Sub 2536 A=0.5237 G=0.4763, T=0.0000
African Others Sub 96 A=0.59 G=0.41, T=0.00
African American Sub 2440 A=0.5209 G=0.4791, T=0.0000
Asian Sub 156 A=0.212 G=0.788, T=0.000
East Asian Sub 130 A=0.208 G=0.792, T=0.000
Other Asian Sub 26 A=0.23 G=0.77, T=0.00
Latin American 1 Sub 146 A=0.452 G=0.548, T=0.000
Latin American 2 Sub 610 A=0.331 G=0.669, T=0.000
South Asian Sub 98 A=0.29 G=0.71, T=0.00
Other Sub 916 A=0.388 G=0.612, 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 A=0.415214 G=0.584786
gnomAD - Genomes Global Study-wide 139666 A=0.418420 G=0.581580
gnomAD - Genomes European Sub 75650 A=0.38373 G=0.61627
gnomAD - Genomes African Sub 41820 A=0.50835 G=0.49165
gnomAD - Genomes American Sub 13616 A=0.36207 G=0.63793
gnomAD - Genomes Ashkenazi Jewish Sub 3316 A=0.5498 G=0.4502
gnomAD - Genomes East Asian Sub 3126 A=0.1705 G=0.8295
gnomAD - Genomes Other Sub 2138 A=0.4046 G=0.5954
Allele Frequency Aggregator Total Global 34254 A=0.40451 G=0.59549, T=0.00000
Allele Frequency Aggregator European Sub 29792 A=0.39756 G=0.60244, T=0.00000
Allele Frequency Aggregator African Sub 2536 A=0.5237 G=0.4763, T=0.0000
Allele Frequency Aggregator Other Sub 916 A=0.388 G=0.612, T=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.331 G=0.669, T=0.000
Allele Frequency Aggregator Asian Sub 156 A=0.212 G=0.788, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.452 G=0.548, T=0.000
Allele Frequency Aggregator South Asian Sub 98 A=0.29 G=0.71, T=0.00
14KJPN JAPANESE Study-wide 28256 A=0.19525 G=0.80475
8.3KJPN JAPANESE Study-wide 16758 A=0.19501 G=0.80499
1000Genomes_30x Global Study-wide 6404 A=0.3743 G=0.6257
1000Genomes_30x African Sub 1786 A=0.4983 G=0.5017
1000Genomes_30x Europe Sub 1266 A=0.3847 G=0.6153
1000Genomes_30x South Asian Sub 1202 A=0.4027 G=0.5973
1000Genomes_30x East Asian Sub 1170 A=0.1573 G=0.8427
1000Genomes_30x American Sub 980 A=0.359 G=0.641
1000Genomes Global Study-wide 5008 A=0.3714 G=0.6286
1000Genomes African Sub 1322 A=0.4992 G=0.5008
1000Genomes East Asian Sub 1008 A=0.1617 G=0.8383
1000Genomes Europe Sub 1006 A=0.3867 G=0.6133
1000Genomes South Asian Sub 978 A=0.409 G=0.591
1000Genomes American Sub 694 A=0.357 G=0.643
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.3692 G=0.6308
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.3923 G=0.6077
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.3784 G=0.6216
KOREAN population from KRGDB KOREAN Study-wide 2928 A=0.1933 C=0.0000, G=0.8067, T=0.0000
Korean Genome Project KOREAN Study-wide 1832 A=0.1599 G=0.8401
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.363 G=0.637
Northern Sweden ACPOP Study-wide 600 A=0.448 G=0.552
SGDP_PRJ Global Study-wide 500 A=0.244 G=0.756
Qatari Global Study-wide 216 A=0.435 G=0.565
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.181 G=0.819
Siberian Global Study-wide 42 A=0.26 G=0.74
The Danish reference pan genome Danish Study-wide 40 A=0.35 G=0.65
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.91951257A>C
GRCh38.p14 chr 7 NC_000007.14:g.91951257A>G
GRCh38.p14 chr 7 NC_000007.14:g.91951257A>T
GRCh37.p13 chr 7 NC_000007.13:g.91580571A>C
GRCh37.p13 chr 7 NC_000007.13:g.91580571A>G
GRCh37.p13 chr 7 NC_000007.13:g.91580571A>T
AKAP9 RefSeqGene (LRG_331) NG_011623.1:g.15383A>C
AKAP9 RefSeqGene (LRG_331) NG_011623.1:g.15383A>G
AKAP9 RefSeqGene (LRG_331) NG_011623.1:g.15383A>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+10110A>C N/A Intron Variant
AKAP9 transcript variant 3 NM_147185.3:c.48+10110A>C 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 A= C G T
GRCh38.p14 chr 7 NC_000007.14:g.91951257= NC_000007.14:g.91951257A>C NC_000007.14:g.91951257A>G NC_000007.14:g.91951257A>T
GRCh37.p13 chr 7 NC_000007.13:g.91580571= NC_000007.13:g.91580571A>C NC_000007.13:g.91580571A>G NC_000007.13:g.91580571A>T
AKAP9 RefSeqGene (LRG_331) NG_011623.1:g.15383= NG_011623.1:g.15383A>C NG_011623.1:g.15383A>G NG_011623.1:g.15383A>T
AKAP9 transcript variant 2 NM_005751.4:c.48+10110= NM_005751.4:c.48+10110A>C NM_005751.4:c.48+10110A>G NM_005751.4:c.48+10110A>T
AKAP9 transcript variant 2 NM_005751.5:c.48+10110= NM_005751.5:c.48+10110A>C NM_005751.5:c.48+10110A>G NM_005751.5:c.48+10110A>T
AKAP9 transcript variant 3 NM_147185.2:c.48+10110= NM_147185.2:c.48+10110A>C NM_147185.2:c.48+10110A>G NM_147185.2:c.48+10110A>T
AKAP9 transcript variant 3 NM_147185.3:c.48+10110= NM_147185.3:c.48+10110A>C NM_147185.3:c.48+10110A>G NM_147185.3:c.48+10110A>T
AKAP9 transcript variant X1 XM_005250102.1:c.48+10110= XM_005250102.1:c.48+10110A>C XM_005250102.1:c.48+10110A>G XM_005250102.1:c.48+10110A>T
AKAP9 transcript variant X2 XM_005250103.1:c.48+10110= XM_005250103.1:c.48+10110A>C XM_005250103.1:c.48+10110A>G XM_005250103.1:c.48+10110A>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#.

77 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 KWOK ss419 Sep 19, 2000 (36)
2 YUSUKE ss3222208 Sep 28, 2001 (100)
3 WI_SSAHASNP ss11858569 Jul 11, 2003 (116)
4 CSHL-HAPMAP ss17165271 Feb 27, 2004 (120)
5 ABI ss42899329 Mar 15, 2006 (126)
6 HGSV ss78268199 Dec 07, 2007 (129)
7 HGSV ss81388972 Dec 16, 2007 (130)
8 BCMHGSC_JDW ss93727858 Mar 24, 2008 (129)
9 HUMANGENOME_JCVI ss98318142 Feb 06, 2009 (130)
10 KRIBB_YJKIM ss104796514 Feb 06, 2009 (130)
11 BGI ss105557395 Feb 06, 2009 (130)
12 1000GENOMES ss112352271 Jan 25, 2009 (130)
13 1000GENOMES ss114094386 Jan 25, 2009 (130)
14 ILLUMINA-UK ss116195149 Dec 01, 2009 (131)
15 ENSEMBL ss142682617 Dec 01, 2009 (131)
16 ENSEMBL ss143095237 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss164845242 Jul 04, 2010 (132)
18 BCM-HGSC-SUB ss208049352 Jul 04, 2010 (132)
19 1000GENOMES ss223203767 Jul 14, 2010 (132)
20 1000GENOMES ss234075414 Jul 15, 2010 (132)
21 1000GENOMES ss241011340 Jul 15, 2010 (132)
22 BL ss254516325 May 09, 2011 (134)
23 GMI ss279438211 May 04, 2012 (137)
24 GMI ss285677186 Apr 25, 2013 (138)
25 PJP ss293916398 May 09, 2011 (134)
26 TISHKOFF ss560153051 Apr 25, 2013 (138)
27 SSMP ss654554974 Apr 25, 2013 (138)
28 EVA-GONL ss984538597 Aug 21, 2014 (142)
29 JMKIDD_LAB ss1074794903 Aug 21, 2014 (142)
30 1000GENOMES ss1326135781 Aug 21, 2014 (142)
31 DDI ss1431208825 Apr 01, 2015 (144)
32 EVA_GENOME_DK ss1582306465 Apr 01, 2015 (144)
33 EVA_DECODE ss1594115508 Apr 01, 2015 (144)
34 EVA_UK10K_ALSPAC ss1618693675 Apr 01, 2015 (144)
35 EVA_UK10K_TWINSUK ss1661687708 Apr 01, 2015 (144)
36 HAMMER_LAB ss1805111677 Sep 08, 2015 (146)
37 WEILL_CORNELL_DGM ss1927799983 Feb 12, 2016 (147)
38 GENOMED ss1970760993 Jul 19, 2016 (147)
39 JJLAB ss2024583294 Sep 14, 2016 (149)
40 CSHL ss2136748249 Nov 08, 2017 (151)
41 USC_VALOUEV ss2152804194 Dec 20, 2016 (150)
42 HUMAN_LONGEVITY ss2295781322 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2626783593 Nov 08, 2017 (151)
44 GRF ss2708511476 Nov 08, 2017 (151)
45 ILLUMINA ss2711115376 Nov 08, 2017 (151)
46 GNOMAD ss2856168024 Nov 08, 2017 (151)
47 SWEGEN ss3001625992 Nov 08, 2017 (151)
48 BIOINF_KMB_FNS_UNIBA ss3026085261 Nov 08, 2017 (151)
49 CSHL ss3347731027 Nov 08, 2017 (151)
50 URBANLAB ss3648701387 Oct 12, 2018 (152)
51 EGCUT_WGS ss3669381533 Jul 13, 2019 (153)
52 EVA_DECODE ss3720202815 Jul 13, 2019 (153)
53 ACPOP ss3734860221 Jul 13, 2019 (153)
54 EVA ss3766865042 Jul 13, 2019 (153)
55 PACBIO ss3785892408 Jul 13, 2019 (153)
56 PACBIO ss3791183295 Jul 13, 2019 (153)
57 PACBIO ss3796063257 Jul 13, 2019 (153)
58 KHV_HUMAN_GENOMES ss3810038380 Jul 13, 2019 (153)
59 EVA ss3830700149 Apr 26, 2020 (154)
60 EVA ss3838848895 Apr 26, 2020 (154)
61 EVA ss3844303826 Apr 26, 2020 (154)
62 SGDP_PRJ ss3867878957 Apr 26, 2020 (154)
63 KRGDB ss3915148092 Apr 26, 2020 (154)
64 KOGIC ss3962085782 Apr 26, 2020 (154)
65 TOPMED ss4754733083 Apr 26, 2021 (155)
66 TOMMO_GENOMICS ss5184424759 Apr 26, 2021 (155)
67 1000G_HIGH_COVERAGE ss5273852551 Oct 16, 2022 (156)
68 HUGCELL_USP ss5470840231 Oct 16, 2022 (156)
69 EVA ss5509048681 Oct 16, 2022 (156)
70 1000G_HIGH_COVERAGE ss5562541242 Oct 16, 2022 (156)
71 SANFORD_IMAGENETICS ss5643488549 Oct 16, 2022 (156)
72 TOMMO_GENOMICS ss5725062387 Oct 16, 2022 (156)
73 YY_MCH ss5808883016 Oct 16, 2022 (156)
74 EVA ss5823188227 Oct 16, 2022 (156)
75 EVA ss5856002992 Oct 16, 2022 (156)
76 EVA ss5859883078 Oct 16, 2022 (156)
77 EVA ss5972667070 Oct 16, 2022 (156)
78 1000Genomes NC_000007.13 - 91580571 Oct 12, 2018 (152)
79 1000Genomes_30x NC_000007.14 - 91951257 Oct 16, 2022 (156)
80 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 91580571 Oct 12, 2018 (152)
81 Genetic variation in the Estonian population NC_000007.13 - 91580571 Oct 12, 2018 (152)
82 The Danish reference pan genome NC_000007.13 - 91580571 Apr 26, 2020 (154)
83 gnomAD - Genomes NC_000007.14 - 91951257 Apr 26, 2021 (155)
84 Genome of the Netherlands Release 5 NC_000007.13 - 91580571 Apr 26, 2020 (154)
85 KOREAN population from KRGDB NC_000007.13 - 91580571 Apr 26, 2020 (154)
86 Korean Genome Project NC_000007.14 - 91951257 Apr 26, 2020 (154)
87 Northern Sweden NC_000007.13 - 91580571 Jul 13, 2019 (153)
88 Qatari NC_000007.13 - 91580571 Apr 26, 2020 (154)
89 SGDP_PRJ NC_000007.13 - 91580571 Apr 26, 2020 (154)
90 Siberian NC_000007.13 - 91580571 Apr 26, 2020 (154)
91 8.3KJPN NC_000007.13 - 91580571 Apr 26, 2021 (155)
92 14KJPN NC_000007.14 - 91951257 Oct 16, 2022 (156)
93 TopMed NC_000007.14 - 91951257 Apr 26, 2021 (155)
94 UK 10K study - Twins NC_000007.13 - 91580571 Oct 12, 2018 (152)
95 A Vietnamese Genetic Variation Database NC_000007.13 - 91580571 Jul 13, 2019 (153)
96 ALFA NC_000007.14 - 91951257 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)
rs61201646 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
22325486, ss3915148092 NC_000007.13:91580570:A:C NC_000007.14:91951256:A:C (self)
ss78268199, ss81388972 NC_000007.11:91225221:A:G NC_000007.14:91951256:A:G (self)
ss93727858, ss112352271, ss114094386, ss116195149, ss164845242, ss208049352, ss254516325, ss279438211, ss285677186, ss293916398, ss1594115508, ss2136748249 NC_000007.12:91418506:A:G NC_000007.14:91951256:A:G (self)
38142201, 21224327, 15119781, 8471404, 9476994, 22325486, 8145086, 9841913, 19895937, 5320548, 42394066, 21224327, 4734341, ss223203767, ss234075414, ss241011340, ss560153051, ss654554974, ss984538597, ss1074794903, ss1326135781, ss1431208825, ss1582306465, ss1618693675, ss1661687708, ss1805111677, ss1927799983, ss1970760993, ss2024583294, ss2152804194, ss2626783593, ss2708511476, ss2711115376, ss2856168024, ss3001625992, ss3347731027, ss3669381533, ss3734860221, ss3766865042, ss3785892408, ss3791183295, ss3796063257, ss3830700149, ss3838848895, ss3867878957, ss3915148092, ss5184424759, ss5509048681, ss5643488549, ss5823188227, ss5972667070 NC_000007.13:91580570:A:G NC_000007.14:91951256:A:G (self)
50067177, 269107473, 18463783, 58899491, 592110642, 13239400340, ss2295781322, ss3026085261, ss3648701387, ss3720202815, ss3810038380, ss3844303826, ss3962085782, ss4754733083, ss5273852551, ss5470840231, ss5562541242, ss5725062387, ss5808883016, ss5856002992, ss5859883078 NC_000007.14:91951256:A:G NC_000007.14:91951256:A:G (self)
ss11858569 NT_007933.12:16814786:A:G NC_000007.14:91951256:A:G (self)
ss17165271 NT_007933.13:16814786:A:G NC_000007.14:91951256:A:G (self)
ss419, ss3222208, ss42899329, ss98318142, ss104796514, ss105557395, ss142682617, ss143095237 NT_007933.15:29613413:A:G NC_000007.14:91951256:A:G (self)
22325486, ss3915148092 NC_000007.13:91580570:A:T NC_000007.14:91951256:A:T (self)
13239400340 NC_000007.14:91951256:A:T NC_000007.14:91951256: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 rs416

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