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dbSNP Short Genetic Variations

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.

rs2002555

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr12:53423453 (GRCh38.p12) 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=0.16168 (20302/125568, TOPMED)
G=0.1580 (4958/31370, GnomAD)
G=0.157 (784/5008, 1000G) (+ 5 more)
G=0.173 (774/4480, Estonian)
G=0.183 (707/3854, ALSPAC)
G=0.179 (663/3708, TWINSUK)
G=0.14 (87/600, NorthernSweden)
G=0.07 (14/210, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
AMHR2 : 2KB Upstream Variant
Publications
15 citations
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.p12 chr 12 NC_000012.12:g.53423453A>G
GRCh37.p13 chr 12 NC_000012.11:g.53817237A>G
AMHR2 RefSeqGene NG_015981.1:g.4599A>G
Gene: AMHR2, anti-Mullerian hormone receptor type 2 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
AMHR2 transcript variant 2 NM_001164690.2:c. N/A Upstream Transcript Variant
AMHR2 transcript variant 3 NM_001164691.2:c. N/A Upstream Transcript Variant
AMHR2 transcript variant 1 NM_020547.3:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X1 XM_011538173.1:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X2 XM_011538174.1:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X3 XM_011538176.1:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X4 XM_011538178.1:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X5 XM_011538179.1:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X6 XM_011538180.1:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X7 XM_011538181.1:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X10 XM_011538183.2:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X11 XM_011538184.2:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X12 XM_011538185.1:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X13 XM_011538186.3:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X9 XM_017019179.2:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X8 XM_024448938.1:c. N/A Upstream Transcript Variant
AMHR2 transcript variant X14 XR_002957309.1:n. N/A Upstream Transcript Variant
AMHR2 transcript variant X15 XR_002957310.1:n. N/A Upstream Transcript Variant
AMHR2 transcript variant X16 XR_002957311.1:n. N/A Upstream Transcript Variant
AMHR2 transcript variant X17 XR_002957312.1:n. N/A 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
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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 125568 A=0.83832 G=0.16168
gnomAD - Genomes Global Study-wide 31370 A=0.8420 G=0.1580
gnomAD - Genomes European Sub 18882 A=0.8288 G=0.1712
gnomAD - Genomes African Sub 8712 A=0.871 G=0.129
gnomAD - Genomes East Asian Sub 1556 A=0.835 G=0.165
gnomAD - Genomes Other Sub 1086 A=0.847 G=0.153
gnomAD - Genomes American Sub 846 A=0.84 G=0.16
gnomAD - Genomes Ashkenazi Jewish Sub 288 A=0.85 G=0.15
1000Genomes Global Study-wide 5008 A=0.843 G=0.157
1000Genomes African Sub 1322 A=0.877 G=0.123
1000Genomes East Asian Sub 1008 A=0.836 G=0.164
1000Genomes Europe Sub 1006 A=0.836 G=0.164
1000Genomes South Asian Sub 978 A=0.84 G=0.16
1000Genomes American Sub 694 A=0.80 G=0.20
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.827 G=0.173
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.817 G=0.183
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.821 G=0.179
Northern Sweden ACPOP Study-wide 600 A=0.85 G=0.14
A Vietnamese Genetic Variation Database Global Study-wide 210 A=0.93 G=0.07
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 Note
GRCh38.p12 chr 12 NC_000012.12:g.53423453= NC_000012.12:g.53423453A>G
GRCh37.p13 chr 12 NC_000012.11:g.53817237= NC_000012.11:g.53817237A>G
AMHR2 RefSeqGene NG_015981.1:g.4599= NG_015981.1:g.4599A>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#.

77 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2917152 Jan 12, 2001 (92)
2 PERLEGEN ss23960065 Sep 20, 2004 (123)
3 ABI ss38949292 Mar 14, 2006 (126)
4 PERLEGEN ss69109475 May 16, 2007 (127)
5 ILLUMINA ss75109747 Dec 06, 2007 (129)
6 HUMANGENOME_JCVI ss97310298 Feb 05, 2009 (130)
7 ILLUMINA-UK ss118815919 Feb 14, 2009 (130)
8 KRIBB_YJKIM ss119411707 Dec 01, 2009 (131)
9 ENSEMBL ss143948815 Dec 01, 2009 (131)
10 ILLUMINA ss160487268 Dec 01, 2009 (131)
11 ILLUMINA ss173038639 Jul 04, 2010 (132)
12 BUSHMAN ss198197766 Jul 04, 2010 (132)
13 BCM-HGSC-SUB ss208223315 Jul 04, 2010 (132)
14 1000GENOMES ss211285187 Jul 14, 2010 (132)
15 1000GENOMES ss225759709 Jul 14, 2010 (132)
16 1000GENOMES ss235939919 Jul 15, 2010 (132)
17 1000GENOMES ss242498504 Jul 15, 2010 (132)
18 GMI ss281401367 May 04, 2012 (137)
19 PJP ss291253362 May 09, 2011 (134)
20 ILLUMINA ss480377379 May 04, 2012 (137)
21 ILLUMINA ss480389798 May 04, 2012 (137)
22 ILLUMINA ss481164529 Sep 08, 2015 (146)
23 ILLUMINA ss484986271 May 04, 2012 (137)
24 ILLUMINA ss537021407 Sep 08, 2015 (146)
25 TISHKOFF ss563173789 Apr 25, 2013 (138)
26 SSMP ss658730146 Apr 25, 2013 (138)
27 ILLUMINA ss778849675 Sep 08, 2015 (146)
28 ILLUMINA ss782939451 Sep 08, 2015 (146)
29 ILLUMINA ss783902081 Sep 08, 2015 (146)
30 ILLUMINA ss832195028 Sep 08, 2015 (146)
31 ILLUMINA ss834310317 Sep 08, 2015 (146)
32 EVA-GONL ss989546387 Aug 21, 2014 (142)
33 JMKIDD_LAB ss1078469920 Aug 21, 2014 (142)
34 1000GENOMES ss1345067223 Aug 21, 2014 (142)
35 DDI ss1426937241 Apr 01, 2015 (144)
36 EVA_GENOME_DK ss1576291546 Apr 01, 2015 (144)
37 EVA_DECODE ss1599218387 Apr 01, 2015 (144)
38 EVA_UK10K_ALSPAC ss1628617229 Apr 01, 2015 (144)
39 EVA_UK10K_TWINSUK ss1671611262 Apr 01, 2015 (144)
40 EVA_SVP ss1713328771 Apr 01, 2015 (144)
41 ILLUMINA ss1752072416 Sep 08, 2015 (146)
42 WEILL_CORNELL_DGM ss1932911186 Feb 12, 2016 (147)
43 GENOMED ss1967592995 Jul 19, 2016 (147)
44 JJLAB ss2027206858 Sep 14, 2016 (149)
45 USC_VALOUEV ss2155545661 Dec 20, 2016 (150)
46 HUMAN_LONGEVITY ss2189890693 Dec 20, 2016 (150)
47 TOPMED ss2353826764 Dec 20, 2016 (150)
48 SYSTEMSBIOZJU ss2628084547 Nov 08, 2017 (151)
49 ILLUMINA ss2632961065 Nov 08, 2017 (151)
50 GRF ss2699888950 Nov 08, 2017 (151)
51 GNOMAD ss2910645508 Nov 08, 2017 (151)
52 AFFY ss2985617238 Nov 08, 2017 (151)
53 SWEGEN ss3009709721 Nov 08, 2017 (151)
54 BIOINF_KMB_FNS_UNIBA ss3027412205 Nov 08, 2017 (151)
55 TOPMED ss3171222540 Nov 08, 2017 (151)
56 CSHL ss3350070365 Nov 08, 2017 (151)
57 ILLUMINA ss3626881077 Oct 12, 2018 (152)
58 ILLUMINA ss3630970118 Oct 12, 2018 (152)
59 ILLUMINA ss3633020900 Oct 12, 2018 (152)
60 ILLUMINA ss3633721889 Oct 12, 2018 (152)
61 ILLUMINA ss3634505627 Oct 12, 2018 (152)
62 ILLUMINA ss3635412641 Oct 12, 2018 (152)
63 ILLUMINA ss3636190651 Oct 12, 2018 (152)
64 ILLUMINA ss3637163630 Oct 12, 2018 (152)
65 ILLUMINA ss3637964039 Oct 12, 2018 (152)
66 ILLUMINA ss3640212960 Oct 12, 2018 (152)
67 ILLUMINA ss3641030543 Oct 12, 2018 (152)
68 ILLUMINA ss3641325266 Oct 12, 2018 (152)
69 ILLUMINA ss3642957563 Oct 12, 2018 (152)
70 URBANLAB ss3649840976 Oct 12, 2018 (152)
71 EGCUT_WGS ss3676980980 Jul 13, 2019 (153)
72 EVA_DECODE ss3693696427 Jul 13, 2019 (153)
73 ACPOP ss3739033530 Jul 13, 2019 (153)
74 ILLUMINA ss3744806303 Jul 13, 2019 (153)
75 EVA ss3750496065 Jul 13, 2019 (153)
76 ILLUMINA ss3772305760 Jul 13, 2019 (153)
77 KHV_HUMAN_GENOMES ss3815825061 Jul 13, 2019 (153)
78 1000Genomes NC_000012.11 - 53817237 Oct 12, 2018 (152)
79 The Avon Longitudinal Study of Parents and Children NC_000012.11 - 53817237 Oct 12, 2018 (152)
80 Genetic variation in the Estonian population NC_000012.11 - 53817237 Oct 12, 2018 (152)
81 gnomAD - Genomes NC_000012.11 - 53817237 Jul 13, 2019 (153)
82 Northern Sweden NC_000012.11 - 53817237 Jul 13, 2019 (153)
83 TopMed NC_000012.12 - 53423453 Oct 12, 2018 (152)
84 UK 10K study - Twins NC_000012.11 - 53817237 Oct 12, 2018 (152)
85 A Vietnamese Genetic Variation Database NC_000012.11 - 53817237 Jul 13, 2019 (153)
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)
rs17098994 Oct 08, 2004 (123)
rs386552171 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss118815919, ss198197766, ss208223315, ss211285187, ss281401367, ss291253362, ss480377379, ss1599218387, ss1713328771, ss3642957563 NC_000012.10:52103503:A:G NC_000012.12:53423452:A:G (self)
57817915, 32104123, 22719228, 157795962, 12318395, 32104123, 7127033, ss225759709, ss235939919, ss242498504, ss480389798, ss481164529, ss484986271, ss537021407, ss563173789, ss658730146, ss778849675, ss782939451, ss783902081, ss832195028, ss834310317, ss989546387, ss1078469920, ss1345067223, ss1426937241, ss1576291546, ss1628617229, ss1671611262, ss1752072416, ss1932911186, ss1967592995, ss2027206858, ss2155545661, ss2353826764, ss2628084547, ss2632961065, ss2699888950, ss2910645508, ss2985617238, ss3009709721, ss3350070365, ss3626881077, ss3630970118, ss3633020900, ss3633721889, ss3634505627, ss3635412641, ss3636190651, ss3637163630, ss3637964039, ss3640212960, ss3641030543, ss3641325266, ss3676980980, ss3739033530, ss3744806303, ss3750496065, ss3772305760 NC_000012.11:53817236:A:G NC_000012.12:53423452:A:G (self)
84056862, ss2189890693, ss3027412205, ss3171222540, ss3649840976, ss3693696427, ss3815825061 NC_000012.12:53423452:A:G NC_000012.12:53423452:A:G (self)
ss2917152, ss23960065, ss38949292, ss69109475, ss75109747, ss97310298, ss119411707, ss143948815, ss160487268, ss173038639 NT_029419.12:15960542:A:G NC_000012.12:53423452: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.

15 citations for rs2002555
PMID Title Author Year Journal
17636279 A polymorphism in the AMH type II receptor gene is associated with age at menopause in interaction with parity. Kevenaar ME et al. 2007 Human reproduction (Oxford, England)
18230658 A functional anti-mullerian hormone gene polymorphism is associated with follicle number and androgen levels in polycystic ovary syndrome patients. Kevenaar ME et al. 2008 The Journal of clinical endocrinology and metabolism
18603647 Functional genetic polymorphisms and female reproductive disorders: Part I: Polycystic ovary syndrome and ovarian response. Simoni M et al. 2008 Human reproduction update
20236105 Association study of four key folliculogenesis genes in polycystic ovary syndrome. Sproul K et al. 2010 BJOG
20734064 A large-scale candidate gene association study of age at menarche and age at natural menopause. He C et al. 2010 Human genetics
21193543 Genes involved in initial follicle recruitment may be associated with age at menopause. Voorhuis M et al. 2011 The Journal of clinical endocrinology and metabolism
22701696 Genetic polymorphisms influence the ovarian response to rFSH stimulation in patients undergoing in vitro fertilization programs with ICSI. Boudjenah R et al. 2012 PloS one
23424626 Genetic variation and reproductive timing: African American women from the Population Architecture using Genomics and Epidemiology (PAGE) Study. Spencer KL et al. 2013 PloS one
23544102 Interactions between genetic variants in AMH and AMHR2 may modify age at natural menopause. Braem MG et al. 2013 PloS one
23969185 Increased frequency of the anti-mullerian-inhibiting hormone receptor 2 (AMHR2) 482 A>G polymorphism in women with polycystic ovary syndrome: relationship to luteinizing hormone levels. Georgopoulos NA et al. 2013 The Journal of clinical endocrinology and metabolism
25379134 Genetic variants in anti-Mullerian hormone and anti-Mullerian hormone receptor genes and breast cancer risk in Caucasians and African Americans. Nan H et al. 2014 International journal of molecular epidemiology and genetics
26243799 Genetics of primary ovarian insufficiency: new developments and opportunities. Qin Y et al. 2015 Human reproduction update
26848671 The Relationship between AMH and AMHR2 Polymorphisms and the Follicular Phase in Late Reproductive Stage Women. Jurczak A et al. 2016 International journal of environmental research and public health
31089932 Anti-Müllerian hormone level is associated with vitamin D receptor polymorphisms in women with polycystic ovary syndrome. Szafarowska M et al. 2019 Journal of assisted reproduction and genetics
31115963 The implication of single-nucleotide polymorphisms in ovarian hyperstimulation syndrome. Ghaderian SMH et al. 2019 Molecular reproduction and development

Genomic regions, transcripts, and products
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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.post246+3cda961