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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.

rs17646919

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr22:30004872 (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=0.057244 (15152/264690, TOPMED)
G=0.077320 (17663/228440, ALFA)
G=0.054558 (7653/140274, GnomAD) (+ 16 more)
G=0.0323 (207/6404, 1000G_30x)
G=0.0292 (146/5008, 1000G)
G=0.0308 (138/4480, Estonian)
G=0.0859 (331/3854, ALSPAC)
G=0.0817 (303/3708, TWINSUK)
G=0.0293 (61/2084, HGDP_Stanford)
G=0.0653 (74/1134, Daghestan)
G=0.075 (75/998, GoNL)
G=0.042 (25/600, NorthernSweden)
G=0.028 (14/496, HapMap)
G=0.065 (14/216, Qatari)
G=0.15 (8/54, Ancient Sardinia)
G=0.12 (5/40, GENOME_DK)
A=0.45 (10/22, SGDP_PRJ)
A=0.5 (2/4, Siberian)
G=0.5 (2/4, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MTMR3 : Intron Variant
Publications
2 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 228534 A=0.922677 G=0.077323
European Sub 199318 A=0.917313 G=0.082687
African Sub 7774 A=0.9843 G=0.0157
African Others Sub 276 A=1.000 G=0.000
African American Sub 7498 A=0.9837 G=0.0163
Asian Sub 796 A=1.000 G=0.000
East Asian Sub 618 A=1.000 G=0.000
Other Asian Sub 178 A=1.000 G=0.000
Latin American 1 Sub 910 A=0.929 G=0.071
Latin American 2 Sub 7026 A=0.9369 G=0.0631
South Asian Sub 5056 A=0.9879 G=0.0121
Other Sub 7654 A=0.9348 G=0.0652


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=0.942756 G=0.057244
Allele Frequency Aggregator Total Global 228440 A=0.922680 G=0.077320
Allele Frequency Aggregator European Sub 199242 A=0.917322 G=0.082678
Allele Frequency Aggregator African Sub 7774 A=0.9843 G=0.0157
Allele Frequency Aggregator Other Sub 7636 A=0.9347 G=0.0653
Allele Frequency Aggregator Latin American 2 Sub 7026 A=0.9369 G=0.0631
Allele Frequency Aggregator South Asian Sub 5056 A=0.9879 G=0.0121
Allele Frequency Aggregator Latin American 1 Sub 910 A=0.929 G=0.071
Allele Frequency Aggregator Asian Sub 796 A=1.000 G=0.000
gnomAD - Genomes Global Study-wide 140274 A=0.945442 G=0.054558
gnomAD - Genomes European Sub 75952 A=0.92555 G=0.07445
gnomAD - Genomes African Sub 42066 A=0.98564 G=0.01436
gnomAD - Genomes American Sub 13654 A=0.92552 G=0.07448
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.9268 G=0.0732
gnomAD - Genomes East Asian Sub 3130 A=0.9997 G=0.0003
gnomAD - Genomes Other Sub 2152 A=0.9382 G=0.0618
1000Genomes_30x Global Study-wide 6404 A=0.9677 G=0.0323
1000Genomes_30x African Sub 1786 A=0.9972 G=0.0028
1000Genomes_30x Europe Sub 1266 A=0.8981 G=0.1019
1000Genomes_30x South Asian Sub 1202 A=0.9975 G=0.0025
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.929 G=0.071
1000Genomes Global Study-wide 5008 A=0.9708 G=0.0292
1000Genomes African Sub 1322 A=0.9970 G=0.0030
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=0.9056 G=0.0944
1000Genomes South Asian Sub 978 A=0.997 G=0.003
1000Genomes American Sub 694 A=0.937 G=0.063
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.9692 G=0.0308
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9141 G=0.0859
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9183 G=0.0817
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 A=0.9707 G=0.0293
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 A=0.971 G=0.029
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 A=0.954 G=0.046
HGDP-CEPH-db Supplement 1 Europe Sub 320 A=0.897 G=0.103
HGDP-CEPH-db Supplement 1 Africa Sub 242 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 America Sub 216 A=1.000 G=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 A=1.00 G=0.00
Genome-wide autozygosity in Daghestan Global Study-wide 1134 A=0.9347 G=0.0653
Genome-wide autozygosity in Daghestan Daghestan Sub 628 A=0.916 G=0.084
Genome-wide autozygosity in Daghestan Near_East Sub 142 A=0.951 G=0.049
Genome-wide autozygosity in Daghestan Central Asia Sub 122 A=0.975 G=0.025
Genome-wide autozygosity in Daghestan Europe Sub 108 A=0.917 G=0.083
Genome-wide autozygosity in Daghestan South Asian Sub 98 A=1.00 G=0.00
Genome-wide autozygosity in Daghestan Caucasus Sub 36 A=0.94 G=0.06
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.925 G=0.075
Northern Sweden ACPOP Study-wide 600 A=0.958 G=0.042
HapMap Global Study-wide 496 A=0.972 G=0.028
HapMap American Sub 286 A=0.951 G=0.049
HapMap African Sub 120 A=1.000 G=0.000
HapMap Asian Sub 90 A=1.00 G=0.00
Qatari Global Study-wide 216 A=0.935 G=0.065
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 54 A=0.85 G=0.15
The Danish reference pan genome Danish Study-wide 40 A=0.88 G=0.12
SGDP_PRJ Global Study-wide 22 A=0.45 G=0.55
Siberian Global Study-wide 4 A=0.5 G=0.5
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 22 NC_000022.11:g.30004872A>G
GRCh37.p13 chr 22 NC_000022.10:g.30400861A>G
Gene: MTMR3, myotubularin related protein 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MTMR3 transcript variant 3 NM_021090.4:c.671+1879A>G N/A Intron Variant
MTMR3 transcript variant 1 NM_153050.3:c.671+1879A>G N/A Intron Variant
MTMR3 transcript variant 2 NM_153051.3:c.671+1879A>G 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 22 NC_000022.11:g.30004872= NC_000022.11:g.30004872A>G
GRCh37.p13 chr 22 NC_000022.10:g.30400861= NC_000022.10:g.30400861A>G
MTMR3 transcript variant 3 NM_021090.3:c.671+1879= NM_021090.3:c.671+1879A>G
MTMR3 transcript variant 3 NM_021090.4:c.671+1879= NM_021090.4:c.671+1879A>G
MTMR3 transcript variant 1 NM_153050.2:c.671+1879= NM_153050.2:c.671+1879A>G
MTMR3 transcript variant 1 NM_153050.3:c.671+1879= NM_153050.3:c.671+1879A>G
MTMR3 transcript variant 2 NM_153051.2:c.671+1879= NM_153051.2:c.671+1879A>G
MTMR3 transcript variant 2 NM_153051.3:c.671+1879= NM_153051.3:c.671+1879A>G
MTMR3 transcript variant X1 XM_005261803.1:c.710+1879= XM_005261803.1:c.710+1879A>G
MTMR3 transcript variant X2 XM_005261804.1:c.710+1879= XM_005261804.1:c.710+1879A>G
MTMR3 transcript variant X3 XM_005261805.1:c.710+1879= XM_005261805.1:c.710+1879A>G
MTMR3 transcript variant X4 XM_005261806.1:c.671+1879= XM_005261806.1:c.671+1879A>G
MTMR3 transcript variant X5 XM_005261807.1:c.710+1879= XM_005261807.1:c.710+1879A>G
MTMR3 transcript variant X6 XM_005261808.1:c.710+1879= XM_005261808.1:c.710+1879A>G
MTMR3 transcript variant X7 XM_005261809.1:c.257+1879= XM_005261809.1:c.257+1879A>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#.

93 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss24585294 Sep 20, 2004 (123)
2 AFFY ss66479584 Dec 01, 2006 (127)
3 ILLUMINA ss66803469 Dec 01, 2006 (127)
4 ILLUMINA ss67190575 Dec 01, 2006 (127)
5 ILLUMINA ss67571146 Dec 01, 2006 (127)
6 PERLEGEN ss69274606 May 18, 2007 (127)
7 ILLUMINA ss70668711 May 24, 2008 (130)
8 ILLUMINA ss71230815 May 18, 2007 (127)
9 ILLUMINA ss75863749 Dec 06, 2007 (129)
10 AFFY ss76293991 Dec 06, 2007 (129)
11 ILLUMINA ss79092226 Dec 14, 2007 (130)
12 KRIBB_YJKIM ss85396175 Dec 14, 2007 (130)
13 ILLUMINA ss121803091 Dec 01, 2009 (131)
14 ILLUMINA ss153701479 Dec 01, 2009 (131)
15 ILLUMINA ss159322924 Dec 01, 2009 (131)
16 ILLUMINA ss160451248 Dec 01, 2009 (131)
17 ILLUMINA ss170798923 Jul 04, 2010 (132)
18 ILLUMINA ss172867423 Jul 04, 2010 (132)
19 1000GENOMES ss238050539 Jul 15, 2010 (132)
20 ILLUMINA ss480264634 May 04, 2012 (137)
21 ILLUMINA ss480275596 May 04, 2012 (137)
22 ILLUMINA ss481020902 Sep 08, 2015 (146)
23 ILLUMINA ss484930251 May 04, 2012 (137)
24 ILLUMINA ss536978222 Sep 08, 2015 (146)
25 ILLUMINA ss778837727 Aug 21, 2014 (142)
26 ILLUMINA ss782911439 Aug 21, 2014 (142)
27 ILLUMINA ss783874640 Aug 21, 2014 (142)
28 ILLUMINA ss825422744 Apr 01, 2015 (144)
29 ILLUMINA ss832166398 Apr 01, 2015 (144)
30 ILLUMINA ss832834951 Aug 21, 2014 (142)
31 ILLUMINA ss833425781 Aug 21, 2014 (142)
32 ILLUMINA ss834298248 Aug 21, 2014 (142)
33 EVA-GONL ss995301736 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1082623485 Aug 21, 2014 (142)
35 1000GENOMES ss1366982863 Aug 21, 2014 (142)
36 HAMMER_LAB ss1397784269 Sep 08, 2015 (146)
37 DDI ss1429242962 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1579733304 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1639896352 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1682890385 Apr 01, 2015 (144)
41 EVA_DECODE ss1699370900 Apr 01, 2015 (144)
42 EVA_SVP ss1713737341 Apr 01, 2015 (144)
43 ILLUMINA ss1752418032 Sep 08, 2015 (146)
44 WEILL_CORNELL_DGM ss1938868202 Feb 12, 2016 (147)
45 JJLAB ss2030205654 Sep 14, 2016 (149)
46 USC_VALOUEV ss2158821858 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2246959106 Dec 20, 2016 (150)
48 ILLUMINA ss2633871903 Nov 08, 2017 (151)
49 ILLUMINA ss2635111672 Nov 08, 2017 (151)
50 ILLUMINA ss2710956030 Nov 08, 2017 (151)
51 GNOMAD ss2973868606 Nov 08, 2017 (151)
52 AFFY ss2985236654 Nov 08, 2017 (151)
53 AFFY ss2985853099 Nov 08, 2017 (151)
54 SWEGEN ss3019226931 Nov 08, 2017 (151)
55 CSHL ss3352815184 Nov 08, 2017 (151)
56 ILLUMINA ss3628522695 Oct 12, 2018 (152)
57 ILLUMINA ss3631823542 Oct 12, 2018 (152)
58 ILLUMINA ss3633271535 Oct 12, 2018 (152)
59 ILLUMINA ss3633987198 Oct 12, 2018 (152)
60 ILLUMINA ss3634865055 Oct 12, 2018 (152)
61 ILLUMINA ss3635671673 Oct 12, 2018 (152)
62 ILLUMINA ss3636560997 Oct 12, 2018 (152)
63 ILLUMINA ss3637423909 Oct 12, 2018 (152)
64 ILLUMINA ss3638379622 Oct 12, 2018 (152)
65 ILLUMINA ss3639193530 Oct 12, 2018 (152)
66 ILLUMINA ss3639613216 Oct 12, 2018 (152)
67 ILLUMINA ss3640572359 Oct 12, 2018 (152)
68 ILLUMINA ss3643339615 Oct 12, 2018 (152)
69 BIOINF_KMB_FNS_UNIBA ss3645681582 Oct 12, 2018 (152)
70 ILLUMINA ss3654004576 Oct 12, 2018 (152)
71 EGCUT_WGS ss3685723596 Jul 13, 2019 (153)
72 EVA_DECODE ss3708105385 Jul 13, 2019 (153)
73 ACPOP ss3743891408 Jul 13, 2019 (153)
74 ILLUMINA ss3745164912 Jul 13, 2019 (153)
75 ILLUMINA ss3772660843 Jul 13, 2019 (153)
76 PACBIO ss3788815765 Jul 13, 2019 (153)
77 PACBIO ss3793683628 Jul 13, 2019 (153)
78 PACBIO ss3798570079 Jul 13, 2019 (153)
79 KHV_HUMAN_GENOMES ss3822489807 Jul 13, 2019 (153)
80 HGDP ss3847687492 Apr 27, 2020 (154)
81 SGDP_PRJ ss3890447751 Apr 27, 2020 (154)
82 EVA ss3985914761 Apr 27, 2021 (155)
83 EVA ss4017878045 Apr 27, 2021 (155)
84 TOPMED ss5107624310 Apr 27, 2021 (155)
85 1000G_HIGH_COVERAGE ss5310939036 Oct 16, 2022 (156)
86 EVA ss5441009160 Oct 16, 2022 (156)
87 HUGCELL_USP ss5502795518 Oct 16, 2022 (156)
88 1000G_HIGH_COVERAGE ss5618421341 Oct 16, 2022 (156)
89 SANFORD_IMAGENETICS ss5664404859 Oct 16, 2022 (156)
90 EVA ss5800039788 Oct 16, 2022 (156)
91 EVA ss5822007191 Oct 16, 2022 (156)
92 EVA ss5881638044 Oct 16, 2022 (156)
93 EVA ss5959255951 Oct 16, 2022 (156)
94 1000Genomes NC_000022.10 - 30400861 Oct 12, 2018 (152)
95 1000Genomes_30x NC_000022.11 - 30004872 Oct 16, 2022 (156)
96 The Avon Longitudinal Study of Parents and Children NC_000022.10 - 30400861 Oct 12, 2018 (152)
97 Genome-wide autozygosity in Daghestan NC_000022.9 - 28730861 Apr 27, 2020 (154)
98 Genetic variation in the Estonian population NC_000022.10 - 30400861 Oct 12, 2018 (152)
99 The Danish reference pan genome NC_000022.10 - 30400861 Apr 27, 2020 (154)
100 gnomAD - Genomes NC_000022.11 - 30004872 Apr 27, 2021 (155)
101 Genome of the Netherlands Release 5 NC_000022.10 - 30400861 Apr 27, 2020 (154)
102 HGDP-CEPH-db Supplement 1 NC_000022.9 - 28730861 Apr 27, 2020 (154)
103 HapMap NC_000022.11 - 30004872 Apr 27, 2020 (154)
104 Northern Sweden NC_000022.10 - 30400861 Jul 13, 2019 (153)
105 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000022.10 - 30400861 Apr 27, 2021 (155)
106 Qatari NC_000022.10 - 30400861 Apr 27, 2020 (154)
107 SGDP_PRJ NC_000022.10 - 30400861 Apr 27, 2020 (154)
108 Siberian NC_000022.10 - 30400861 Apr 27, 2020 (154)
109 TopMed NC_000022.11 - 30004872 Apr 27, 2021 (155)
110 UK 10K study - Twins NC_000022.10 - 30400861 Oct 12, 2018 (152)
111 ALFA NC_000022.11 - 30004872 Apr 27, 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)
rs57716157 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3639193530, ss3639613216 NC_000022.8:28725414:A:G NC_000022.11:30004871:A:G (self)
298249, 365384, ss160451248, ss480264634, ss825422744, ss1397784269, ss1699370900, ss1713737341, ss2635111672, ss3643339615, ss3847687492 NC_000022.9:28730860:A:G NC_000022.11:30004871:A:G (self)
80528125, 44540308, 31461844, 5898243, 19848097, 17176273, 1140688, 20910124, 42464731, 11338212, 44540308, ss238050539, ss480275596, ss481020902, ss484930251, ss536978222, ss778837727, ss782911439, ss783874640, ss832166398, ss832834951, ss833425781, ss834298248, ss995301736, ss1082623485, ss1366982863, ss1429242962, ss1579733304, ss1639896352, ss1682890385, ss1752418032, ss1938868202, ss2030205654, ss2158821858, ss2633871903, ss2710956030, ss2973868606, ss2985236654, ss2985853099, ss3019226931, ss3352815184, ss3628522695, ss3631823542, ss3633271535, ss3633987198, ss3634865055, ss3635671673, ss3636560997, ss3637423909, ss3638379622, ss3640572359, ss3654004576, ss3685723596, ss3743891408, ss3745164912, ss3772660843, ss3788815765, ss3793683628, ss3798570079, ss3890447751, ss3985914761, ss4017878045, ss5441009160, ss5664404859, ss5800039788, ss5822007191, ss5959255951 NC_000022.10:30400860:A:G NC_000022.11:30004871:A:G (self)
105947276, 568661108, 2243951, 382733257, 6069653944, ss2246959106, ss3645681582, ss3708105385, ss3822489807, ss5107624310, ss5310939036, ss5502795518, ss5618421341, ss5881638044 NC_000022.11:30004871:A:G NC_000022.11:30004871:A:G (self)
ss24585294, ss66479584, ss66803469, ss67190575, ss67571146, ss69274606, ss70668711, ss71230815, ss75863749, ss76293991, ss79092226, ss85396175, ss121803091, ss153701479, ss159322924, ss170798923, ss172867423 NT_011520.12:9791429:A:G NC_000022.11:30004871: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.

2 citations for rs17646919
PMID Title Author Year Journal
19300500 A genome-wide association study of pulmonary function measures in the Framingham Heart Study. Wilk JB et al. 2009 PLoS genetics
22424883 Genome-wide association study of lung function decline in adults with and without asthma. Imboden M et al. 2012 The Journal of allergy and clinical immunology
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