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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.

rs2232169

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:172447967 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.037946 (10044/264690, TOPMED)
C=0.036672 (5144/140270, GnomAD)
C=0.02275 (1129/49624, ALFA) (+ 14 more)
C=0.04252 (553/13006, GO-ESP)
C=0.0320 (205/6404, 1000G_30x)
C=0.0315 (158/5008, 1000G)
C=0.0241 (108/4480, Estonian)
C=0.0236 (91/3854, ALSPAC)
C=0.0262 (97/3708, TWINSUK)
C=0.024 (24/998, GoNL)
C=0.028 (17/600, NorthernSweden)
C=0.017 (9/534, MGP)
C=0.017 (5/294, FINRISK)
C=0.093 (20/216, Qatari)
G=0.048 (10/210, HapMap)
C=0.03 (1/40, GENOME_DK)
G=0.32 (7/22, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
GHSR : Synonymous Variant
Publications
4 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 49624 G=0.97725 A=0.00000, C=0.02275 0.954861 0.000363 0.044777 1
European Sub 38018 G=0.97756 A=0.00000, C=0.02244 0.955442 0.000316 0.044242 1
African Sub 3188 G=0.9862 A=0.0000, C=0.0138 0.973024 0.000627 0.026349 1
African Others Sub 114 G=0.991 A=0.000, C=0.009 0.982456 0.0 0.017544 0
African American Sub 3074 G=0.9860 A=0.0000, C=0.0140 0.972674 0.000651 0.026675 1
Asian Sub 168 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A
East Asian Sub 112 G=1.000 A=0.000, C=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 56 G=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 494 G=0.966 A=0.000, C=0.034 0.931174 0.0 0.068826 0
Latin American 2 Sub 608 G=0.998 A=0.000, C=0.002 0.996711 0.0 0.003289 0
South Asian Sub 90 G=1.00 A=0.00, C=0.00 1.0 0.0 0.0 N/A
Other Sub 7058 G=0.9697 A=0.0000, C=0.0303 0.939926 0.000567 0.059507 0


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 G=0.962054 C=0.037946
gnomAD - Genomes Global Study-wide 140270 G=0.963328 C=0.036672
gnomAD - Genomes European Sub 75958 G=0.97559 C=0.02441
gnomAD - Genomes African Sub 42042 G=0.93319 C=0.06681
gnomAD - Genomes American Sub 13662 G=0.97819 C=0.02181
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9708 C=0.0292
gnomAD - Genomes East Asian Sub 3134 G=0.9997 C=0.0003
gnomAD - Genomes Other Sub 2150 G=0.9605 C=0.0395
Allele Frequency Aggregator Total Global 49624 G=0.97725 A=0.00000, C=0.02275
Allele Frequency Aggregator European Sub 38018 G=0.97756 A=0.00000, C=0.02244
Allele Frequency Aggregator Other Sub 7058 G=0.9697 A=0.0000, C=0.0303
Allele Frequency Aggregator African Sub 3188 G=0.9862 A=0.0000, C=0.0138
Allele Frequency Aggregator Latin American 2 Sub 608 G=0.998 A=0.000, C=0.002
Allele Frequency Aggregator Latin American 1 Sub 494 G=0.966 A=0.000, C=0.034
Allele Frequency Aggregator Asian Sub 168 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 90 G=1.00 A=0.00, C=0.00
GO Exome Sequencing Project Global Study-wide 13006 G=0.95748 C=0.04252
GO Exome Sequencing Project European American Sub 8600 G=0.9707 C=0.0293
GO Exome Sequencing Project African American Sub 4406 G=0.9317 C=0.0683
1000Genomes_30x Global Study-wide 6404 G=0.9678 A=0.0002, C=0.0320
1000Genomes_30x African Sub 1786 G=0.9345 A=0.0000, C=0.0655
1000Genomes_30x Europe Sub 1266 G=0.9724 A=0.0000, C=0.0276
1000Genomes_30x South Asian Sub 1202 G=0.9725 A=0.0008, C=0.0266
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000, C=0.0000
1000Genomes_30x American Sub 980 G=0.979 A=0.000, C=0.021
1000Genomes Global Study-wide 5008 G=0.9685 C=0.0315
1000Genomes African Sub 1322 G=0.9342 C=0.0658
1000Genomes East Asian Sub 1008 G=1.0000 C=0.0000
1000Genomes Europe Sub 1006 G=0.9722 C=0.0278
1000Genomes South Asian Sub 978 G=0.972 C=0.028
1000Genomes American Sub 694 G=0.977 C=0.023
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9759 C=0.0241
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9764 C=0.0236
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9738 C=0.0262
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.976 C=0.024
Northern Sweden ACPOP Study-wide 600 G=0.972 C=0.028
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.983 C=0.017
FINRISK Finnish from FINRISK project Study-wide 294 G=0.983 C=0.017
Qatari Global Study-wide 216 G=0.907 C=0.093
HapMap Global Study-wide 210 G=0.048 C=0.952
HapMap African Sub 120 G=0.083 C=0.917
HapMap Asian Sub 90 G=0.00 C=1.00
The Danish reference pan genome Danish Study-wide 40 G=0.97 C=0.03
SGDP_PRJ Global Study-wide 22 G=0.32 C=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 3 NC_000003.12:g.172447967G>A
GRCh38.p14 chr 3 NC_000003.12:g.172447967G>C
GRCh37.p13 chr 3 NC_000003.11:g.172165757G>A
GRCh37.p13 chr 3 NC_000003.11:g.172165757G>C
GHSR RefSeqGene NG_021159.1:g.5490C>T
GHSR RefSeqGene NG_021159.1:g.5490C>G
Gene: GHSR, growth hormone secretagogue receptor (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GHSR transcript variant 1a NM_198407.2:c.447C>T L [CTC] > L [CTT] Coding Sequence Variant
growth hormone secretagogue receptor type 1 isoform 1a NP_940799.1:p.Leu149= L (Leu) > L (Leu) Synonymous Variant
GHSR transcript variant 1a NM_198407.2:c.447C>G L [CTC] > L [CTG] Coding Sequence Variant
growth hormone secretagogue receptor type 1 isoform 1a NP_940799.1:p.Leu149= L (Leu) > L (Leu) Synonymous Variant
GHSR transcript variant 1b NM_004122.2:c.447C>T L [CTC] > L [CTT] Coding Sequence Variant
growth hormone secretagogue receptor type 1 isoform 1b NP_004113.1:p.Leu149= L (Leu) > L (Leu) Synonymous Variant
GHSR transcript variant 1b NM_004122.2:c.447C>G L [CTC] > L [CTG] Coding Sequence Variant
growth hormone secretagogue receptor type 1 isoform 1b NP_004113.1:p.Leu149= L (Leu) > L (Leu) 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: C (allele ID: 290311 )
ClinVar Accession Disease Names Clinical Significance
RCV000404209.3 Short stature due to growth hormone secretagogue receptor deficiency Benign
RCV001691981.4 not provided Benign
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 G= A C
GRCh38.p14 chr 3 NC_000003.12:g.172447967= NC_000003.12:g.172447967G>A NC_000003.12:g.172447967G>C
GRCh37.p13 chr 3 NC_000003.11:g.172165757= NC_000003.11:g.172165757G>A NC_000003.11:g.172165757G>C
GHSR RefSeqGene NG_021159.1:g.5490= NG_021159.1:g.5490C>T NG_021159.1:g.5490C>G
GHSR transcript variant 1a NM_198407.2:c.447= NM_198407.2:c.447C>T NM_198407.2:c.447C>G
GHSR transcript variant 1b NM_004122.2:c.447= NM_004122.2:c.447C>T NM_004122.2:c.447C>G
growth hormone secretagogue receptor type 1 isoform 1a NP_940799.1:p.Leu149= NP_940799.1:p.Leu149= NP_940799.1:p.Leu149=
growth hormone secretagogue receptor type 1 isoform 1b NP_004113.1:p.Leu149= NP_004113.1:p.Leu149= NP_004113.1:p.Leu149=
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#.

65 SubSNP, 21 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 GENAISSANCE ss3179439 Aug 15, 2001 (98)
2 IARC-GAN ss7844195 Mar 31, 2003 (113)
3 HG_BONN_CNS_SNPS ss12587069 Aug 26, 2003 (117)
4 PERLEGEN ss23320528 Sep 20, 2004 (123)
5 APPLERA_GI ss48417340 Mar 14, 2006 (126)
6 SEATTLESEQ ss159706536 Dec 01, 2009 (131)
7 ILLUMINA ss160517892 Dec 01, 2009 (131)
8 BUSHMAN ss203531901 Jul 04, 2010 (132)
9 1000GENOMES ss220582235 Jul 14, 2010 (132)
10 1000GENOMES ss232145154 Jul 14, 2010 (132)
11 NHLBI-ESP ss342152281 May 09, 2011 (134)
12 ILLUMINA ss481285901 Sep 08, 2015 (146)
13 1000GENOMES ss490878093 May 04, 2012 (137)
14 GSK-GENETICS ss491268999 May 04, 2012 (137)
15 CLINSEQ_SNP ss491845526 May 04, 2012 (137)
16 ILLUMINA ss536055701 Sep 08, 2015 (146)
17 JMKIDD_LAB ss974450695 Aug 21, 2014 (142)
18 EVA-GONL ss979461333 Aug 21, 2014 (142)
19 JMKIDD_LAB ss1067457042 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1071058310 Aug 21, 2014 (142)
21 1000GENOMES ss1307294361 Aug 21, 2014 (142)
22 EVA_GENOME_DK ss1580298532 Apr 01, 2015 (144)
23 EVA_FINRISK ss1584031610 Apr 01, 2015 (144)
24 EVA_DECODE ss1588955989 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1608816644 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1651810677 Apr 01, 2015 (144)
27 EVA_EXAC ss1687295683 Apr 01, 2015 (144)
28 EVA_EXAC ss1687295684 Apr 01, 2015 (144)
29 EVA_MGP ss1711041405 Apr 01, 2015 (144)
30 WEILL_CORNELL_DGM ss1922681546 Feb 12, 2016 (147)
31 JJLAB ss2021916148 Sep 14, 2016 (149)
32 HUMAN_LONGEVITY ss2258207229 Dec 20, 2016 (150)
33 GNOMAD ss2734203854 Nov 08, 2017 (151)
34 GNOMAD ss2747140532 Nov 08, 2017 (151)
35 GNOMAD ss2802394765 Nov 08, 2017 (151)
36 AFFY ss2985276626 Nov 08, 2017 (151)
37 SWEGEN ss2993651419 Nov 08, 2017 (151)
38 ILLUMINA ss3628836862 Oct 12, 2018 (152)
39 ILLUMINA ss3636626360 Oct 12, 2018 (152)
40 ILLUMINA ss3654046550 Oct 12, 2018 (152)
41 EGCUT_WGS ss3661600679 Jul 13, 2019 (153)
42 EVA_DECODE ss3710837126 Jul 13, 2019 (153)
43 ACPOP ss3730597583 Jul 13, 2019 (153)
44 EVA ss3761042263 Jul 13, 2019 (153)
45 KHV_HUMAN_GENOMES ss3804177500 Jul 13, 2019 (153)
46 EVA ss3823974672 Apr 25, 2020 (154)
47 EVA ss3825646917 Apr 25, 2020 (154)
48 EVA ss3828220700 Apr 25, 2020 (154)
49 SGDP_PRJ ss3857570048 Apr 25, 2020 (154)
50 FSA-LAB ss3984268157 Apr 26, 2021 (155)
51 FSA-LAB ss3984268158 Apr 26, 2021 (155)
52 EVA ss3986261938 Apr 26, 2021 (155)
53 TOPMED ss4593579314 Apr 26, 2021 (155)
54 EVA ss5237002013 Apr 26, 2021 (155)
55 EVA ss5237640836 Oct 12, 2022 (156)
56 1000G_HIGH_COVERAGE ss5257018509 Oct 12, 2022 (156)
57 EVA ss5345083510 Oct 12, 2022 (156)
58 HUGCELL_USP ss5456063033 Oct 12, 2022 (156)
59 EVA ss5507312658 Oct 12, 2022 (156)
60 1000G_HIGH_COVERAGE ss5536986577 Oct 12, 2022 (156)
61 SANFORD_IMAGENETICS ss5633758640 Oct 12, 2022 (156)
62 EVA ss5826863850 Oct 12, 2022 (156)
63 EVA ss5848597313 Oct 12, 2022 (156)
64 EVA ss5872143155 Oct 12, 2022 (156)
65 EVA ss5962135581 Oct 12, 2022 (156)
66 1000Genomes NC_000003.11 - 172165757 Oct 12, 2018 (152)
67 1000Genomes_30x NC_000003.12 - 172447967 Oct 12, 2022 (156)
68 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 172165757 Oct 12, 2018 (152)
69 Genetic variation in the Estonian population NC_000003.11 - 172165757 Oct 12, 2018 (152)
70 ExAC

Submission ignored due to conflicting rows:
Row 7242675 (NC_000003.11:172165756:G:G 117139/120732, NC_000003.11:172165756:G:C 3593/120732)
Row 7242676 (NC_000003.11:172165756:G:G 120731/120732, NC_000003.11:172165756:G:A 1/120732)

- Oct 12, 2018 (152)
71 ExAC

Submission ignored due to conflicting rows:
Row 7242675 (NC_000003.11:172165756:G:G 117139/120732, NC_000003.11:172165756:G:C 3593/120732)
Row 7242676 (NC_000003.11:172165756:G:G 120731/120732, NC_000003.11:172165756:G:A 1/120732)

- Oct 12, 2018 (152)
72 FINRISK NC_000003.11 - 172165757 Apr 25, 2020 (154)
73 The Danish reference pan genome NC_000003.11 - 172165757 Apr 25, 2020 (154)
74 gnomAD - Genomes NC_000003.12 - 172447967 Apr 26, 2021 (155)
75 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 3296376 (NC_000003.11:172165756:G:G 250953/250954, NC_000003.11:172165756:G:A 1/250954)
Row 3296377 (NC_000003.11:172165756:G:G 243999/250954, NC_000003.11:172165756:G:C 6955/250954)

- Jul 13, 2019 (153)
76 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 3296376 (NC_000003.11:172165756:G:G 250953/250954, NC_000003.11:172165756:G:A 1/250954)
Row 3296377 (NC_000003.11:172165756:G:G 243999/250954, NC_000003.11:172165756:G:C 6955/250954)

- Jul 13, 2019 (153)
77 GO Exome Sequencing Project NC_000003.11 - 172165757 Oct 12, 2018 (152)
78 Genome of the Netherlands Release 5 NC_000003.11 - 172165757 Apr 25, 2020 (154)
79 HapMap NC_000003.12 - 172447967 Apr 25, 2020 (154)
80 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 172165757 Apr 25, 2020 (154)
81 Northern Sweden NC_000003.11 - 172165757 Jul 13, 2019 (153)
82 Qatari NC_000003.11 - 172165757 Apr 25, 2020 (154)
83 SGDP_PRJ NC_000003.11 - 172165757 Apr 25, 2020 (154)
84 TopMed NC_000003.12 - 172447967 Apr 26, 2021 (155)
85 UK 10K study - Twins NC_000003.11 - 172165757 Oct 12, 2018 (152)
86 ALFA NC_000003.12 - 172447967 Apr 26, 2021 (155)
87 ClinVar RCV000404209.3 Oct 12, 2022 (156)
88 ClinVar RCV001691981.4 Oct 12, 2022 (156)
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)
rs16845630 Oct 07, 2004 (123)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1687295684, ss2734203854 NC_000003.11:172165756:G:A NC_000003.12:172447966:G:A (self)
24512512, 5218613792, ss5536986577 NC_000003.12:172447966:G:A NC_000003.12:172447966:G:A (self)
ss160517892, ss203531901, ss491268999, ss491845526, ss1588955989 NC_000003.10:173648450:G:C NC_000003.12:172447966:G:C (self)
18601443, 10365190, 7338927, 28071, 6463471, 432949, 4555608, 157165, 3882448, 4723476, 9587028, 10365190, ss220582235, ss232145154, ss342152281, ss481285901, ss490878093, ss536055701, ss974450695, ss979461333, ss1067457042, ss1071058310, ss1307294361, ss1580298532, ss1584031610, ss1608816644, ss1651810677, ss1687295683, ss1711041405, ss1922681546, ss2021916148, ss2734203854, ss2747140532, ss2802394765, ss2985276626, ss2993651419, ss3628836862, ss3636626360, ss3654046550, ss3661600679, ss3730597583, ss3761042263, ss3823974672, ss3825646917, ss3828220700, ss3857570048, ss3984268157, ss3984268158, ss3986261938, ss5345083510, ss5507312658, ss5633758640, ss5826863850, ss5848597313, ss5962135581 NC_000003.11:172165756:G:C NC_000003.12:172447966:G:C (self)
RCV000404209.3, RCV001691981.4, 24512512, 132142029, 2510532, 430956869, 5218613792, ss2258207229, ss3710837126, ss3804177500, ss4593579314, ss5237002013, ss5237640836, ss5257018509, ss5456063033, ss5536986577, ss5872143155 NC_000003.12:172447966:G:C NC_000003.12:172447966:G:C (self)
ss3179439, ss7844195, ss12587069, ss23320528, ss48417340, ss159706536 NT_005612.16:78660902:G:C NC_000003.12:172447966:G:C (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

4 citations for rs2232169
PMID Title Author Year Journal
18647811 Ghrelin receptor gene polymorphisms and body size in children and adults. Garcia EA et al. 2008 The Journal of clinical endocrinology and metabolism
19165163 Association studies on ghrelin and ghrelin receptor gene polymorphisms with obesity. Gueorguiev M et al. 2009 Obesity (Silver Spring, Md.)
19876004 Obesity-related polymorphisms and their associations with the ability to regulate fat oxidation in obese Europeans: the NUGENOB study. Corpeleijn E et al. 2010 Obesity (Silver Spring, Md.)
20404923 Family and population-based studies of variation within the ghrelin receptor locus in relation to measures of obesity. Gjesing AP et al. 2010 PloS one
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.post820+afb47a3d