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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.

rs4900

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr19:3119241 (GRCh38.p13) 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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.378235 (100115/264690, TOPMED)
T=0.427221 (107299/251156, GnomAD_exome)
T=0.379040 (53055/139972, GnomAD) (+ 18 more)
T=0.426275 (51714/121316, ExAC)
T=0.44609 (28489/63864, ALFA)
T=0.46605 (7811/16760, 8.3KJPN)
T=0.38221 (4971/13006, GO-ESP)
T=0.3488 (1747/5008, 1000G)
T=0.4529 (2029/4480, Estonian)
C=0.4982 (1920/3854, ALSPAC)
T=0.4768 (1768/3708, TWINSUK)
T=0.4242 (1243/2930, KOREAN)
T=0.387 (238/615, Vietnamese)
C=0.480 (288/600, NorthernSweden)
T=0.444 (237/534, MGP)
C=0.360 (128/356, SGDP_PRJ)
T=0.322 (103/320, HapMap)
T=0.441 (134/304, FINRISK)
T=0.477 (103/216, Qatari)
C=0.34 (15/44, Siberian)
C=0.42 (17/40, GENOME_DK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
GNA11 : Synonymous 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.p13 chr 19 NC_000019.10:g.3119241C>T
GRCh37.p13 chr 19 NC_000019.9:g.3119239C>T
GNA11 RefSeqGene (LRG_1111) NG_033852.2:g.29832C>T
Gene: GNA11, G protein subunit alpha 11 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GNA11 transcript NM_002067.5:c.771C>T T [ACC] > T [ACT] Coding Sequence Variant
guanine nucleotide-binding protein subunit alpha-11 NP_002058.2:p.Thr257= T (Thr) > T (Thr) Synonymous 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.

Allele: T (allele ID: 256851 )
ClinVar Accession Disease Names Clinical Significance
RCV000245998.2 not specified Benign

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 63864 C=0.55391 T=0.44609
European Sub 47226 C=0.52948 T=0.47052
African Sub 5200 C=0.7673 T=0.2327
African Others Sub 180 C=0.789 T=0.211
African American Sub 5020 C=0.7665 T=0.2335
Asian Sub 206 C=0.602 T=0.398
East Asian Sub 142 C=0.620 T=0.380
Other Asian Sub 64 C=0.56 T=0.44
Latin American 1 Sub 836 C=0.616 T=0.384
Latin American 2 Sub 684 C=0.608 T=0.392
South Asian Sub 144 C=0.604 T=0.396
Other Sub 9568 C=0.5474 T=0.4526


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=0.621765 T=0.378235
gnomAD - Exomes Global Study-wide 251156 C=0.572779 T=0.427221
gnomAD - Exomes European Sub 135312 C=0.539974 T=0.460026
gnomAD - Exomes Asian Sub 48868 C=0.58337 T=0.41663
gnomAD - Exomes American Sub 34552 C=0.57846 T=0.42154
gnomAD - Exomes African Sub 16242 C=0.78974 T=0.21026
gnomAD - Exomes Ashkenazi Jewish Sub 10060 C=0.59841 T=0.40159
gnomAD - Exomes Other Sub 6122 C=0.5635 T=0.4365
gnomAD - Genomes Global Study-wide 139972 C=0.620960 T=0.379040
gnomAD - Genomes European Sub 75794 C=0.54069 T=0.45931
gnomAD - Genomes African Sub 41958 C=0.78235 T=0.21765
gnomAD - Genomes American Sub 13630 C=0.58423 T=0.41577
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=0.5858 T=0.4142
gnomAD - Genomes East Asian Sub 3124 C=0.5925 T=0.4075
gnomAD - Genomes Other Sub 2146 C=0.6295 T=0.3705
ExAC Global Study-wide 121316 C=0.573725 T=0.426275
ExAC Europe Sub 73314 C=0.53994 T=0.46006
ExAC Asian Sub 25132 C=0.57978 T=0.42022
ExAC American Sub 11574 C=0.58113 T=0.41887
ExAC African Sub 10390 C=0.78537 T=0.21463
ExAC Other Sub 906 C=0.618 T=0.382
8.3KJPN JAPANESE Study-wide 16760 C=0.53395 T=0.46605
GO Exome Sequencing Project Global Study-wide 13006 C=0.61779 T=0.38221
GO Exome Sequencing Project European American Sub 8600 C=0.5313 T=0.4687
GO Exome Sequencing Project African American Sub 4406 C=0.7867 T=0.2133
1000Genomes Global Study-wide 5008 C=0.6512 T=0.3488
1000Genomes African Sub 1322 C=0.8343 T=0.1657
1000Genomes East Asian Sub 1008 C=0.5942 T=0.4058
1000Genomes Europe Sub 1006 C=0.5676 T=0.4324
1000Genomes South Asian Sub 978 C=0.585 T=0.415
1000Genomes American Sub 694 C=0.599 T=0.401
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.5471 T=0.4529
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.4982 T=0.5018
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.5232 T=0.4768
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.5758 T=0.4242
A Vietnamese Genetic Variation Database Global Study-wide 615 C=0.613 T=0.387
Northern Sweden ACPOP Study-wide 600 C=0.480 T=0.520
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.556 T=0.444
SGDP_PRJ Global Study-wide 356 C=0.360 T=0.640
HapMap Global Study-wide 320 C=0.678 T=0.322
HapMap African Sub 116 C=0.862 T=0.138
HapMap American Sub 116 C=0.612 T=0.388
HapMap Asian Sub 88 C=0.52 T=0.48
FINRISK Finnish from FINRISK project Study-wide 304 C=0.559 T=0.441
Qatari Global Study-wide 216 C=0.523 T=0.477
Siberian Global Study-wide 44 C=0.34 T=0.66
The Danish reference pan genome Danish Study-wide 40 C=0.42 T=0.57
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= T
GRCh38.p13 chr 19 NC_000019.10:g.3119241= NC_000019.10:g.3119241C>T
GRCh37.p13 chr 19 NC_000019.9:g.3119239= NC_000019.9:g.3119239C>T
GNA11 RefSeqGene (LRG_1111) NG_033852.2:g.29832= NG_033852.2:g.29832C>T
GNA11 transcript NM_002067.5:c.771= NM_002067.5:c.771C>T
GNA11 transcript NM_002067.4:c.771= NM_002067.4:c.771C>T
GNA11 transcript NM_002067.2:c.771= NM_002067.2:c.771C>T
guanine nucleotide-binding protein subunit alpha-11 NP_002058.2:p.Thr257= NP_002058.2:p.Thr257=
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#.

94 SubSNP, 21 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 KWOK ss396048 Jul 12, 2000 (92)
2 SC_JCM ss570445 Jul 16, 2000 (92)
3 KWOK ss1208088 Oct 04, 2000 (92)
4 KWOK ss1634169 Oct 18, 2000 (92)
5 YUSUKE ss2989693 Jun 15, 2001 (96)
6 SC_SNP ss16188983 Feb 27, 2004 (120)
7 CSHL-HAPMAP ss16790591 Feb 27, 2004 (120)
8 PERLEGEN ss24201629 Sep 20, 2004 (123)
9 ABI ss41027968 Mar 14, 2006 (126)
10 ILLUMINA ss65718886 Oct 16, 2006 (127)
11 SI_EXO ss76894169 Dec 07, 2007 (129)
12 BCMHGSC_JDW ss90884416 Mar 24, 2008 (129)
13 BGI ss103418652 Dec 01, 2009 (131)
14 1000GENOMES ss110995693 Jan 25, 2009 (130)
15 ILLUMINA-UK ss117620585 Feb 14, 2009 (130)
16 ILLUMINA ss120241208 Dec 01, 2009 (131)
17 ENSEMBL ss137520453 Dec 01, 2009 (131)
18 GMI ss155540602 Dec 01, 2009 (131)
19 SEATTLESEQ ss159737955 Dec 01, 2009 (131)
20 ILLUMINA ss160725520 Dec 01, 2009 (131)
21 BUSHMAN ss203601665 Jul 04, 2010 (132)
22 BCM-HGSC-SUB ss208379468 Jul 04, 2010 (132)
23 1000GENOMES ss228013696 Jul 14, 2010 (132)
24 1000GENOMES ss237581780 Jul 15, 2010 (132)
25 1000GENOMES ss243808367 Jul 15, 2010 (132)
26 BL ss255441012 May 09, 2011 (134)
27 GMI ss283101561 May 04, 2012 (137)
28 NHLBI-ESP ss342480272 May 09, 2011 (134)
29 ILLUMINA ss482106268 Sep 08, 2015 (146)
30 ILLUMINA ss483809473 May 04, 2012 (137)
31 ILLUMINA ss484196423 May 04, 2012 (137)
32 1000GENOMES ss491144839 May 04, 2012 (137)
33 CLINSEQ_SNP ss491754048 May 04, 2012 (137)
34 TISHKOFF ss565815771 Apr 25, 2013 (138)
35 SSMP ss661668178 Apr 25, 2013 (138)
36 ILLUMINA ss782544168 Sep 08, 2015 (146)
37 JMKIDD_LAB ss974503095 Aug 21, 2014 (142)
38 EVA-GONL ss994024456 Aug 21, 2014 (142)
39 JMKIDD_LAB ss1067581724 Aug 21, 2014 (142)
40 JMKIDD_LAB ss1081718546 Aug 21, 2014 (142)
41 1000GENOMES ss1362112473 Aug 21, 2014 (142)
42 DDI ss1428315635 Apr 01, 2015 (144)
43 EVA_GENOME_DK ss1578530406 Apr 01, 2015 (144)
44 EVA_FINRISK ss1584112667 Apr 01, 2015 (144)
45 EVA_UK10K_ALSPAC ss1637452483 Apr 01, 2015 (144)
46 EVA_UK10K_TWINSUK ss1680446516 Apr 01, 2015 (144)
47 EVA_EXAC ss1693256462 Apr 01, 2015 (144)
48 EVA_MGP ss1711492693 Apr 01, 2015 (144)
49 HAMMER_LAB ss1809178590 Sep 08, 2015 (146)
50 WEILL_CORNELL_DGM ss1937502397 Feb 12, 2016 (147)
51 GENOMED ss1966658580 Feb 12, 2016 (147)
52 JJLAB ss2029526282 Sep 14, 2016 (149)
53 USC_VALOUEV ss2158040075 Dec 20, 2016 (150)
54 HUMAN_LONGEVITY ss2223805150 Dec 20, 2016 (150)
55 TOPMED ss2389230273 Dec 20, 2016 (150)
56 SYSTEMSBIOZJU ss2629261872 Nov 08, 2017 (151)
57 GRF ss2702643438 Nov 08, 2017 (151)
58 GNOMAD ss2743460562 Nov 08, 2017 (151)
59 GNOMAD ss2750014648 Nov 08, 2017 (151)
60 GNOMAD ss2959749330 Nov 08, 2017 (151)
61 AFFY ss2985764479 Nov 08, 2017 (151)
62 SWEGEN ss3016983865 Nov 08, 2017 (151)
63 EVA_SAMSUNG_MC ss3023071436 Nov 08, 2017 (151)
64 BIOINF_KMB_FNS_UNIBA ss3028595474 Nov 08, 2017 (151)
65 TOPMED ss3286279148 Nov 08, 2017 (151)
66 CSHL ss3352166465 Nov 08, 2017 (151)
67 ILLUMINA ss3636409730 Oct 12, 2018 (152)
68 OMUKHERJEE_ADBS ss3646526994 Oct 12, 2018 (152)
69 EGCUT_WGS ss3683830931 Jul 13, 2019 (153)
70 EVA_DECODE ss3702212927 Jul 13, 2019 (153)
71 ACPOP ss3742798260 Jul 13, 2019 (153)
72 EVA ss3755737323 Jul 13, 2019 (153)
73 PACBIO ss3788449827 Jul 13, 2019 (153)
74 PACBIO ss3793372833 Jul 13, 2019 (153)
75 PACBIO ss3798259377 Jul 13, 2019 (153)
76 KHV_HUMAN_GENOMES ss3820991356 Jul 13, 2019 (153)
77 EVA ss3825215305 Apr 27, 2020 (154)
78 EVA ss3825532221 Apr 27, 2020 (154)
79 EVA ss3825546826 Apr 27, 2020 (154)
80 EVA ss3825921519 Apr 27, 2020 (154)
81 EVA ss3835317364 Apr 27, 2020 (154)
82 EVA ss3841281003 Apr 27, 2020 (154)
83 EVA ss3846784927 Apr 27, 2020 (154)
84 SGDP_PRJ ss3887622944 Apr 27, 2020 (154)
85 KRGDB ss3937557496 Apr 27, 2020 (154)
86 FSA-LAB ss3984138744 Apr 26, 2021 (155)
87 EVA ss3986768357 Apr 26, 2021 (155)
88 TOPMED ss5066009444 Apr 26, 2021 (155)
89 TOMMO_GENOMICS ss5226424300 Apr 26, 2021 (155)
90 CPQ_GEN_INCA ss5236854308 Apr 26, 2021 (155)
91 CPQ_GEN_INCA ss5236858373 Apr 26, 2021 (155)
92 CPQ_GEN_INCA ss5236858374 Apr 26, 2021 (155)
93 EVA ss5236953336 Apr 26, 2021 (155)
94 EVA ss5237244183 Apr 26, 2021 (155)
95 1000Genomes NC_000019.9 - 3119239 Oct 12, 2018 (152)
96 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 3119239 Oct 12, 2018 (152)
97 Genetic variation in the Estonian population NC_000019.9 - 3119239 Oct 12, 2018 (152)
98 ExAC NC_000019.9 - 3119239 Oct 12, 2018 (152)
99 FINRISK NC_000019.9 - 3119239 Apr 27, 2020 (154)
100 The Danish reference pan genome NC_000019.9 - 3119239 Apr 27, 2020 (154)
101 gnomAD - Genomes NC_000019.10 - 3119241 Apr 26, 2021 (155)
102 gnomAD - Exomes NC_000019.9 - 3119239 Jul 13, 2019 (153)
103 GO Exome Sequencing Project NC_000019.9 - 3119239 Oct 12, 2018 (152)
104 HapMap NC_000019.10 - 3119241 Apr 27, 2020 (154)
105 KOREAN population from KRGDB NC_000019.9 - 3119239 Apr 27, 2020 (154)
106 Medical Genome Project healthy controls from Spanish population NC_000019.9 - 3119239 Apr 27, 2020 (154)
107 Northern Sweden NC_000019.9 - 3119239 Jul 13, 2019 (153)
108 Qatari NC_000019.9 - 3119239 Apr 27, 2020 (154)
109 SGDP_PRJ NC_000019.9 - 3119239 Apr 27, 2020 (154)
110 Siberian NC_000019.9 - 3119239 Apr 27, 2020 (154)
111 8.3KJPN NC_000019.9 - 3119239 Apr 26, 2021 (155)
112 TopMed NC_000019.10 - 3119241 Apr 26, 2021 (155)
113 UK 10K study - Twins NC_000019.9 - 3119239 Oct 12, 2018 (152)
114 A Vietnamese Genetic Variation Database NC_000019.9 - 3119239 Jul 13, 2019 (153)
115 ALFA NC_000019.10 - 3119241 Apr 26, 2021 (155)
116 ClinVar RCV000245998.2 Oct 12, 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)
rs308045 Jan 18, 2001 (92)
rs1042622 Jan 18, 2001 (92)
rs2230313 Mar 26, 2002 (103)
rs3182080 Jul 03, 2002 (106)
rs11549608 Oct 08, 2004 (123)
rs17828934 Oct 08, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss90884416, ss110995693, ss117620585, ss203601665, ss208379468, ss255441012, ss283101561, ss483809473, ss491754048 NC_000019.8:3070238:C:T NC_000019.10:3119240:C:T (self)
75480426, 41833995, 29569179, 3736017, 109128, 4717356, 12772924, 1672306, 44734890, 608453, 16083125, 19544319, 39639924, 10556429, 84393607, 41833995, 9250818, ss228013696, ss237581780, ss243808367, ss342480272, ss482106268, ss484196423, ss491144839, ss565815771, ss661668178, ss782544168, ss974503095, ss994024456, ss1067581724, ss1081718546, ss1362112473, ss1428315635, ss1578530406, ss1584112667, ss1637452483, ss1680446516, ss1693256462, ss1711492693, ss1809178590, ss1937502397, ss1966658580, ss2029526282, ss2158040075, ss2389230273, ss2629261872, ss2702643438, ss2743460562, ss2750014648, ss2959749330, ss2985764479, ss3016983865, ss3023071436, ss3352166465, ss3636409730, ss3646526994, ss3683830931, ss3742798260, ss3755737323, ss3788449827, ss3793372833, ss3798259377, ss3825215305, ss3825532221, ss3825546826, ss3825921519, ss3835317364, ss3841281003, ss3887622944, ss3937557496, ss3984138744, ss3986768357, ss5226424300, ss5236854308, ss5236858373, ss5236858374 NC_000019.9:3119238:C:T NC_000019.10:3119240:C:T (self)
RCV000245998.2, 532302089, 1659902, 175659675, 281555108, 5375576570, ss2223805150, ss3028595474, ss3286279148, ss3702212927, ss3820991356, ss3846784927, ss5066009444, ss5236953336, ss5237244183 NC_000019.10:3119240:C:T NC_000019.10:3119240:C:T (self)
ss396048, ss570445, ss1208088, ss1634169, ss2989693, ss16188983, ss16790591, ss24201629, ss41027968, ss65718886, ss76894169, ss103418652, ss120241208, ss137520453, ss155540602, ss159737955, ss160725520 NT_011255.14:3059238:C:T NC_000019.10:3119240: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.

1 citation for rs4900
PMID Title Author Year Journal
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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.post596+ae089ad