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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.

rs10407022

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr19:2249478 (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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.23436 (55345/236156, GnomAD_exome)
G=0.27252 (34220/125568, TOPMED)
G=0.21241 (22281/104896, ExAC) (+ 8 more)
G=0.2570 (8039/31280, GnomAD)
G=0.2605 (3384/12988, GO-ESP)
G=0.324 (1623/5008, 1000G)
G=0.169 (758/4480, Estonian)
G=0.163 (630/3854, ALSPAC)
G=0.161 (598/3708, TWINSUK)
G=0.48 (293/610, Vietnamese)
G=0.22 (131/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
AMH : Missense Variant
MIR4321 : 2KB Upstream Variant
Publications
14 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 19 NC_000019.10:g.2249478G>T
GRCh37.p13 chr 19 NC_000019.9:g.2249477G>T
AMH RefSeqGene NG_012190.1:g.5365G>T
Gene: AMH, anti-Mullerian hormone (plus strand)
Molecule type Change Amino acid[Codon] SO Term
AMH transcript NM_000479.5:c.146G>T S [AGC] > I [ATC] Coding Sequence Variant
muellerian-inhibiting factor preproprotein NP_000470.3:p.Ser49Ile S (Ser) > I (Ile) Missense Variant
Gene: MIR4321, microRNA 4321 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR4321 transcript NR_036207.1: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.

Allele: T (allele ID: 508921 )
ClinVar Accession Disease Names Clinical Significance
RCV000609747.1 Persistent Mullerian duct syndrome Benign
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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").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 236156 G=0.23436 T=0.76564
gnomAD - Exomes European Sub 125466 G=0.17156 T=0.82844
gnomAD - Exomes Asian Sub 47048 G=0.2857 T=0.7143
gnomAD - Exomes American Sub 33332 G=0.3455 T=0.6545
gnomAD - Exomes African Sub 14706 G=0.4355 T=0.5645
gnomAD - Exomes Ashkenazi Jewish Sub 9786 G=0.138 T=0.862
gnomAD - Exomes Other Sub 5818 G=0.191 T=0.809
TopMed Global Study-wide 125568 G=0.27252 T=0.72748
ExAC Global Study-wide 104896 G=0.21241 T=0.78759
ExAC Europe Sub 63742 G=0.1565 T=0.8435
ExAC Asian Sub 22464 G=0.2577 T=0.7423
ExAC American Sub 9690 G=0.323 T=0.677
ExAC African Sub 8256 G=0.393 T=0.607
ExAC Other Sub 744 G=0.20 T=0.80
gnomAD - Genomes Global Study-wide 31280 G=0.2570 T=0.7430
gnomAD - Genomes European Sub 18834 G=0.1680 T=0.8320
gnomAD - Genomes African Sub 8664 G=0.424 T=0.576
gnomAD - Genomes East Asian Sub 1558 G=0.390 T=0.610
gnomAD - Genomes Other Sub 1086 G=0.235 T=0.765
gnomAD - Genomes American Sub 848 G=0.34 T=0.66
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.17 T=0.83
GO Exome Sequencing Project Global Study-wide 12988 G=0.2605 T=0.7395
GO Exome Sequencing Project European American Sub 8592 G=0.169 T=0.831
GO Exome Sequencing Project African American Sub 4396 G=0.439 T=0.561
1000Genomes Global Study-wide 5008 G=0.324 T=0.676
1000Genomes African Sub 1322 G=0.477 T=0.523
1000Genomes East Asian Sub 1008 G=0.414 T=0.586
1000Genomes Europe Sub 1006 G=0.180 T=0.820
1000Genomes South Asian Sub 978 G=0.19 T=0.81
1000Genomes American Sub 694 G=0.30 T=0.70
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.169 T=0.831
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.163 T=0.837
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.161 T=0.839
A Vietnamese Genetic Variation Database Global Study-wide 610 G=0.48 T=0.52
Northern Sweden ACPOP Study-wide 600 G=0.22 T=0.78
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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= T Note
GRCh38.p12 chr 19 NC_000019.10:g.2249478= NC_000019.10:g.2249478G>T
GRCh37.p13 chr 19 NC_000019.9:g.2249477= NC_000019.9:g.2249477G>T
AMH RefSeqGene NG_012190.1:g.5365= NG_012190.1:g.5365G>T
AMH transcript NM_000479.5:c.146= NM_000479.5:c.146G>T
AMH transcript NM_000479.4:c.146= NM_000479.4:c.146G>T
AMH transcript NM_000479.3:c.146= NM_000479.3:c.146G>T
muellerian-inhibiting factor preproprotein NP_000470.3:p.Ser49= NP_000470.3:p.Ser49Ile
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#.

121 SubSNP, 11 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss14699093 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss16800629 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss20068218 Feb 27, 2004 (120)
4 SSAHASNP ss21529402 Apr 05, 2004 (121)
5 ILLUMINA ss66549010 Dec 02, 2006 (127)
6 ILLUMINA ss66881938 Dec 02, 2006 (127)
7 ILLUMINA ss66974252 Dec 02, 2006 (127)
8 ILLUMINA ss70365091 May 18, 2007 (127)
9 ILLUMINA ss70477645 May 24, 2008 (130)
10 ILLUMINA ss71000764 May 18, 2007 (127)
11 ILLUMINA ss75488151 Dec 06, 2007 (129)
12 HGSV ss78358313 Dec 06, 2007 (129)
13 HGSV ss83294874 Dec 15, 2007 (130)
14 KRIBB_YJKIM ss84934649 Dec 15, 2007 (130)
15 CORNELL ss86243563 Mar 23, 2008 (129)
16 BCMHGSC_JDW ss90881571 Mar 24, 2008 (129)
17 HUMANGENOME_JCVI ss96249102 Feb 05, 2009 (130)
18 1000GENOMES ss114742701 Jan 25, 2009 (130)
19 ILLUMINA-UK ss117618034 Feb 14, 2009 (130)
20 ILLUMINA ss121302273 Dec 01, 2009 (131)
21 ENSEMBL ss136302076 Dec 01, 2009 (131)
22 ENSEMBL ss137515884 Dec 01, 2009 (131)
23 ILLUMINA ss152719363 Dec 01, 2009 (131)
24 ILLUMINA ss159122289 Dec 01, 2009 (131)
25 SEATTLESEQ ss159737886 Dec 01, 2009 (131)
26 ILLUMINA ss159890098 Dec 01, 2009 (131)
27 COMPLETE_GENOMICS ss167661228 Jul 04, 2010 (132)
28 COMPLETE_GENOMICS ss168870199 Jul 04, 2010 (132)
29 ILLUMINA ss169374356 Jul 04, 2010 (132)
30 ILLUMINA ss170031019 Jul 04, 2010 (132)
31 BUSHMAN ss203590758 Jul 04, 2010 (132)
32 BCM-HGSC-SUB ss208432340 Jul 04, 2010 (132)
33 1000GENOMES ss210937647 Jul 14, 2010 (132)
34 1000GENOMES ss228009673 Jul 14, 2010 (132)
35 1000GENOMES ss237579000 Jul 15, 2010 (132)
36 1000GENOMES ss243806168 Jul 15, 2010 (132)
37 GMI ss283098478 May 04, 2012 (137)
38 GMI ss287333874 Apr 25, 2013 (138)
39 PJP ss292173825 May 09, 2011 (134)
40 NHLBI-ESP ss342479661 May 09, 2011 (134)
41 ILLUMINA ss479257923 May 04, 2012 (137)
42 ILLUMINA ss479260848 May 04, 2012 (137)
43 ILLUMINA ss479626255 Sep 08, 2015 (146)
44 ILLUMINA ss484429661 May 04, 2012 (137)
45 1000GENOMES ss491144340 May 04, 2012 (137)
46 EXOME_CHIP ss491536188 May 04, 2012 (137)
47 CLINSEQ_SNP ss491753675 May 04, 2012 (137)
48 TISHKOFF ss565810167 Apr 25, 2013 (138)
49 SSMP ss661662645 Apr 25, 2013 (138)
50 ILLUMINA ss782661289 Sep 08, 2015 (146)
51 ILLUMINA ss783415461 Sep 08, 2015 (146)
52 ILLUMINA ss825334822 Jul 19, 2016 (147)
53 ILLUMINA ss831911799 Sep 08, 2015 (146)
54 ILLUMINA ss832635011 Jul 13, 2019 (153)
55 JMKIDD_LAB ss974503000 Aug 21, 2014 (142)
56 EVA-GONL ss994015781 Aug 21, 2014 (142)
57 JMKIDD_LAB ss1067581447 Aug 21, 2014 (142)
58 JMKIDD_LAB ss1081713201 Aug 21, 2014 (142)
59 1000GENOMES ss1362080314 Aug 21, 2014 (142)
60 DDI ss1428312471 Apr 01, 2015 (144)
61 EVA_GENOME_DK ss1578526794 Apr 01, 2015 (144)
62 EVA_FINRISK ss1584112510 Apr 01, 2015 (144)
63 EVA_UK10K_ALSPAC ss1637437988 Apr 01, 2015 (144)
64 EVA_UK10K_TWINSUK ss1680432021 Apr 01, 2015 (144)
65 EVA_EXAC ss1693245107 Apr 01, 2015 (144)
66 EVA_DECODE ss1698078760 Apr 01, 2015 (144)
67 EVA_MGP ss1711492112 Apr 01, 2015 (144)
68 EVA_SVP ss1713646902 Apr 01, 2015 (144)
69 ILLUMINA ss1752278763 Sep 08, 2015 (146)
70 ILLUMINA ss1752278764 Sep 08, 2015 (146)
71 HAMMER_LAB ss1809174379 Sep 08, 2015 (146)
72 ILLUMINA ss1917929563 Feb 12, 2016 (147)
73 WEILL_CORNELL_DGM ss1937492921 Feb 12, 2016 (147)
74 ILLUMINA ss1946519839 Feb 12, 2016 (147)
75 ILLUMINA ss1959828491 Feb 12, 2016 (147)
76 GENOMED ss1968593141 Jul 19, 2016 (147)
77 JJLAB ss2029521524 Sep 14, 2016 (149)
78 USC_VALOUEV ss2158034365 Dec 20, 2016 (150)
79 HUMAN_LONGEVITY ss2223740781 Dec 20, 2016 (150)
80 TOPMED ss2389162283 Dec 20, 2016 (150)
81 SYSTEMSBIOZJU ss2629259381 Nov 08, 2017 (151)
82 ILLUMINA ss2633509379 Nov 08, 2017 (151)
83 GRF ss2702637906 Nov 08, 2017 (151)
84 ILLUMINA ss2710874719 Nov 08, 2017 (151)
85 GNOMAD ss2743443006 Nov 08, 2017 (151)
86 GNOMAD ss2750008490 Nov 08, 2017 (151)
87 GNOMAD ss2959654281 Nov 08, 2017 (151)
88 SWEGEN ss3016968553 Nov 08, 2017 (151)
89 ILLUMINA ss3021869108 Nov 08, 2017 (151)
90 BIOINF_KMB_FNS_UNIBA ss3028593158 Nov 08, 2017 (151)
91 TOPMED ss3286065872 Nov 08, 2017 (151)
92 CSHL ss3352161990 Nov 08, 2017 (151)
93 ILLUMINA ss3633881890 Oct 12, 2018 (152)
94 ILLUMINA ss3634718735 Oct 12, 2018 (152)
95 ILLUMINA ss3634718736 Oct 12, 2018 (152)
96 ILLUMINA ss3635568952 Oct 12, 2018 (152)
97 ILLUMINA ss3636409323 Oct 12, 2018 (152)
98 ILLUMINA ss3637320620 Oct 12, 2018 (152)
99 ILLUMINA ss3638211463 Oct 12, 2018 (152)
100 ILLUMINA ss3639114315 Oct 12, 2018 (152)
101 ILLUMINA ss3639567013 Oct 12, 2018 (152)
102 ILLUMINA ss3640426043 Oct 12, 2018 (152)
103 ILLUMINA ss3640426044 Oct 12, 2018 (152)
104 ILLUMINA ss3643186079 Oct 12, 2018 (152)
105 ILLUMINA ss3644712159 Oct 12, 2018 (152)
106 OMUKHERJEE_ADBS ss3646526648 Oct 12, 2018 (152)
107 URBANLAB ss3650852873 Oct 12, 2018 (152)
108 ILLUMINA ss3652293096 Oct 12, 2018 (152)
109 EGCUT_WGS ss3683817426 Jul 13, 2019 (153)
110 EVA_DECODE ss3702194756 Jul 13, 2019 (153)
111 ACPOP ss3742790556 Jul 13, 2019 (153)
112 ILLUMINA ss3744456527 Jul 13, 2019 (153)
113 ILLUMINA ss3745018807 Jul 13, 2019 (153)
114 ILLUMINA ss3745018808 Jul 13, 2019 (153)
115 EVA ss3755727625 Jul 13, 2019 (153)
116 ILLUMINA ss3772516224 Jul 13, 2019 (153)
117 ILLUMINA ss3772516225 Jul 13, 2019 (153)
118 PACBIO ss3788447304 Jul 13, 2019 (153)
119 PACBIO ss3793370556 Jul 13, 2019 (153)
120 PACBIO ss3798257103 Jul 13, 2019 (153)
121 KHV_HUMAN_GENOMES ss3820981077 Jul 13, 2019 (153)
122 1000Genomes NC_000019.9 - 2249477 Oct 12, 2018 (152)
123 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 2249477 Oct 12, 2018 (152)
124 Genetic variation in the Estonian population NC_000019.9 - 2249477 Oct 12, 2018 (152)
125 ExAC NC_000019.9 - 2249477 Oct 12, 2018 (152)
126 gnomAD - Genomes NC_000019.9 - 2249477 Jul 13, 2019 (153)
127 gnomAD - Exomes NC_000019.9 - 2249477 Jul 13, 2019 (153)
128 GO Exome Sequencing Project NC_000019.9 - 2249477 Oct 12, 2018 (152)
129 Northern Sweden NC_000019.9 - 2249477 Jul 13, 2019 (153)
130 TopMed NC_000019.10 - 2249478 Oct 12, 2018 (152)
131 UK 10K study - Twins NC_000019.9 - 2249477 Oct 12, 2018 (152)
132 A Vietnamese Genetic Variation Database NC_000019.9 - 2249477 Jul 13, 2019 (153)
133 ClinVar RCV000609747.1 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)
rs58663414 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss78358313, ss83294874, ss90881571, ss114742701, ss117618034, ss167661228, ss168870199, ss203590758, ss208432340, ss210937647, ss283098478, ss287333874, ss292173825, ss479257923, ss491753675, ss825334822, ss1698078760, ss1713646902, ss3639114315, ss3639567013, ss3643186079 NC_000019.8:2200476:G:T NC_000019.10:2249477:G:T (self)
75447101, 41817606, 29555674, 3723771, 205916360, 12755274, 1669766, 16075421, 41817606, 9247676, ss228009673, ss237579000, ss243806168, ss342479661, ss479260848, ss479626255, ss484429661, ss491144340, ss491536188, ss565810167, ss661662645, ss782661289, ss783415461, ss831911799, ss832635011, ss974503000, ss994015781, ss1067581447, ss1081713201, ss1362080314, ss1428312471, ss1578526794, ss1584112510, ss1637437988, ss1680432021, ss1693245107, ss1711492112, ss1752278763, ss1752278764, ss1809174379, ss1917929563, ss1937492921, ss1946519839, ss1959828491, ss1968593141, ss2029521524, ss2158034365, ss2389162283, ss2629259381, ss2633509379, ss2702637906, ss2710874719, ss2743443006, ss2750008490, ss2959654281, ss3016968553, ss3021869108, ss3352161990, ss3633881890, ss3634718735, ss3634718736, ss3635568952, ss3636409323, ss3637320620, ss3638211463, ss3640426043, ss3640426044, ss3644712159, ss3646526648, ss3652293096, ss3683817426, ss3742790556, ss3744456527, ss3745018807, ss3745018808, ss3755727625, ss3772516224, ss3772516225, ss3788447304, ss3793370556, ss3798257103 NC_000019.9:2249476:G:T NC_000019.10:2249477:G:T (self)
RCV000609747.1, 175496968, ss2223740781, ss3028593158, ss3286065872, ss3650852873, ss3702194756, ss3820981077 NC_000019.10:2249477:G:T NC_000019.10:2249477:G:T (self)
ss14699093, ss16800629, ss20068218, ss21529402, ss66549010, ss66881938, ss66974252, ss70365091, ss70477645, ss71000764, ss75488151, ss84934649, ss86243563, ss96249102, ss121302273, ss136302076, ss137515884, ss152719363, ss159122289, ss159737886, ss159890098, ss169374356, ss170031019 NT_011255.14:2189476:G:T NC_000019.10:2249477:G:T (self)
Help

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

14 citations for rs10407022
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
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
23371438 Haplotype analysis of single nucleotide polymorphisms in anti-Müllerian hormone gene in Chinese PCOS women. Xu P et al. 2013 Archives of gynecology and obstetrics
23544102 Interactions between genetic variants in AMH and AMHR2 may modify age at natural menopause. Braem MG et al. 2013 PloS one
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
26464718 Possible involvement of single nucleotide polymorphisms in anti-Müllerian hormone signaling pathway in the pathogenesis of early OHSS in Han Chinese women. Wang L et al. 2015 International journal of clinical and experimental pathology
26604150 Genome-wide association study identifies common and low-frequency variants at the AMH gene locus that strongly predict serum AMH levels in males. Perry JR et al. 2016 Human molecular genetics
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
29358304 The <i>AMH</i> genotype (rs10407022 T&gt;G) is associated with circulating AMH levels in boys, but not in girls. Greiber IK et al. 2018 Endocrine connections
30406448 Could polymorphisms of some hormonal receptor genes, involved in folliculogenesis help in predicting patient response to controlled ovarian stimulation? Čuš M et al. 2019 Journal of assisted reproduction and genetics
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

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