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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.

rs10497189

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr2:157768292 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.072128 (9057/125568, TOPMED)
C=0.09253 (4632/50060, ALFA Project)
C=0.07212 (2264/31392, GnomAD) (+ 16 more)
C=0.0431 (216/5008, 1000G)
C=0.0886 (397/4480, Estonian)
C=0.1077 (415/3854, ALSPAC)
C=0.1001 (371/3708, TWINSUK)
C=0.0451 (132/2930, KOREAN)
C=0.0465 (97/2084, HGDP_Stanford)
C=0.0461 (74/1604, HapMap)
C=0.0889 (101/1136, Daghestan)
C=0.113 (113/998, GoNL)
C=0.046 (29/626, Chileans)
C=0.170 (102/600, NorthernSweden)
C=0.046 (10/216, Qatari)
C=0.037 (8/216, Vietnamese)
T=0.46 (24/52, SGDP_PRJ)
C=0.12 (5/40, GENOME_DK)
T=0.3 (2/6, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ACVR1 : Intron Variant
Publications
2 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 2 NC_000002.12:g.157768292T>C
GRCh37.p13 chr 2 NC_000002.11:g.158624804T>C
ACVR1 RefSeqGene NG_008004.1:g.111820A>G
Gene: ACVR1, activin A receptor type 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ACVR1 transcript variant 1 NM_001105.5:c.790+2076A>G N/A Intron Variant
ACVR1 transcript variant 2 NM_001111067.4:c.790+2076…

NM_001111067.4:c.790+2076A>G

N/A Intron Variant
ACVR1 transcript variant 3 NM_001347663.1:c.790+2076…

NM_001347663.1:c.790+2076A>G

N/A Intron Variant
ACVR1 transcript variant 4 NM_001347664.1:c.790+2076…

NM_001347664.1:c.790+2076A>G

N/A Intron Variant
ACVR1 transcript variant 5 NM_001347665.1:c.790+2076…

NM_001347665.1:c.790+2076A>G

N/A Intron Variant
ACVR1 transcript variant 6 NM_001347666.1:c.790+2076…

NM_001347666.1:c.790+2076A>G

N/A Intron Variant
ACVR1 transcript variant 7 NM_001347667.2:c.790+2076…

NM_001347667.2:c.790+2076A>G

N/A Intron Variant
ACVR1 transcript variant X2 XM_006712825.4:c.790+2076…

XM_006712825.4:c.790+2076A>G

N/A Intron Variant
ACVR1 transcript variant X1 XM_011512108.3:c.790+2076…

XM_011512108.3:c.790+2076A>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

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 76934 T=0.90958 C=0.09042
European Sub 60226 T=0.89687 C=0.10313
African Sub 7838 T=0.9755 C=0.0245
African Others Sub 266 T=0.996 C=0.004
African American Sub 7572 T=0.9748 C=0.0252
Asian Sub 236 T=0.919 C=0.081
East Asian Sub 164 T=0.902 C=0.098
Other Asian Sub 72 T=0.96 C=0.04
Latin American 1 Sub 320 T=0.941 C=0.059
Latin American 2 Sub 1376 T=0.9564 C=0.0436
South Asian Sub 4970 T=0.9372 C=0.0628
Other Sub 1968 T=0.9273 C=0.0727


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 125568 T=0.927872 C=0.072128
ALFA Total Global 50060 T=0.90747 C=0.09253
ALFA European Sub 39016 T=0.89458 C=0.10542
ALFA South Asian Sub 4854 T=0.9368 C=0.0632
ALFA African Sub 4808 T=0.9740 C=0.0260
ALFA Other Sub 968 T=0.937 C=0.063
ALFA Latin American 2 Sub 214 T=0.963 C=0.037
ALFA Asian Sub 116 T=0.922 C=0.078
ALFA Latin American 1 Sub 84 T=0.89 C=0.11
gnomAD - Genomes Global Study-wide 31392 T=0.92788 C=0.07212
gnomAD - Genomes European Sub 18896 T=0.90363 C=0.09637
gnomAD - Genomes African Sub 8714 T=0.9766 C=0.0234
gnomAD - Genomes East Asian Sub 1556 T=0.9428 C=0.0572
gnomAD - Genomes Other Sub 1088 T=0.9246 C=0.0754
gnomAD - Genomes American Sub 848 T=0.952 C=0.048
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.907 C=0.093
1000Genomes Global Study-wide 5008 T=0.9569 C=0.0431
1000Genomes African Sub 1322 T=0.9955 C=0.0045
1000Genomes East Asian Sub 1008 T=0.9554 C=0.0446
1000Genomes Europe Sub 1006 T=0.9185 C=0.0815
1000Genomes South Asian Sub 978 T=0.936 C=0.064
1000Genomes American Sub 694 T=0.971 C=0.029
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.9114 C=0.0886
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.8923 C=0.1077
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.8999 C=0.1001
KOREAN population from KRGDB KOREAN Study-wide 2930 T=0.9549 C=0.0451
HGDP-CEPH-db Supplement 1 Global Study-wide 2084 T=0.9535 C=0.0465
HGDP-CEPH-db Supplement 1 Est_Asia Sub 470 T=0.953 C=0.047
HGDP-CEPH-db Supplement 1 Central_South_Asia Sub 414 T=0.961 C=0.039
HGDP-CEPH-db Supplement 1 Middle_Est Sub 350 T=0.949 C=0.051
HGDP-CEPH-db Supplement 1 Europe Sub 320 T=0.912 C=0.087
HGDP-CEPH-db Supplement 1 Africa Sub 242 T=0.988 C=0.012
HGDP-CEPH-db Supplement 1 America Sub 216 T=1.000 C=0.000
HGDP-CEPH-db Supplement 1 Oceania Sub 72 T=0.86 C=0.14
HapMap Global Study-wide 1604 T=0.9539 C=0.0461
HapMap American Sub 768 T=0.949 C=0.051
HapMap African Sub 406 T=0.973 C=0.027
HapMap Asian Sub 254 T=0.957 C=0.043
HapMap Europe Sub 176 T=0.926 C=0.074
Genome-wide autozygosity in Daghestan Global Study-wide 1136 T=0.9111 C=0.0889
Genome-wide autozygosity in Daghestan Daghestan Sub 628 T=0.889 C=0.111
Genome-wide autozygosity in Daghestan Near_East Sub 144 T=0.938 C=0.062
Genome-wide autozygosity in Daghestan Central Asia Sub 122 T=0.959 C=0.041
Genome-wide autozygosity in Daghestan Europe Sub 108 T=0.935 C=0.065
Genome-wide autozygosity in Daghestan South Asian Sub 98 T=0.91 C=0.09
Genome-wide autozygosity in Daghestan Caucasus Sub 36 T=0.97 C=0.03
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.887 C=0.113
Chileans Chilean Study-wide 626 T=0.954 C=0.046
Northern Sweden ACPOP Study-wide 600 T=0.830 C=0.170
Qatari Global Study-wide 216 T=0.954 C=0.046
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.963 C=0.037
SGDP_PRJ Global Study-wide 52 T=0.46 C=0.54
The Danish reference pan genome Danish Study-wide 40 T=0.88 C=0.12
Siberian Global Study-wide 6 T=0.3 C=0.7
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 T= C
GRCh38.p12 chr 2 NC_000002.12:g.157768292= NC_000002.12:g.157768292T>C
GRCh37.p13 chr 2 NC_000002.11:g.158624804= NC_000002.11:g.158624804T>C
ACVR1 RefSeqGene NG_008004.1:g.111820= NG_008004.1:g.111820A>G
ACVR1 transcript variant 1 NM_001105.4:c.790+2076= NM_001105.4:c.790+2076A>G
ACVR1 transcript variant 1 NM_001105.5:c.790+2076= NM_001105.5:c.790+2076A>G
ACVR1 transcript variant 2 NM_001111067.2:c.790+2076= NM_001111067.2:c.790+2076A>G
ACVR1 transcript variant 2 NM_001111067.4:c.790+2076= NM_001111067.4:c.790+2076A>G
ACVR1 transcript variant 3 NM_001347663.1:c.790+2076= NM_001347663.1:c.790+2076A>G
ACVR1 transcript variant 4 NM_001347664.1:c.790+2076= NM_001347664.1:c.790+2076A>G
ACVR1 transcript variant 5 NM_001347665.1:c.790+2076= NM_001347665.1:c.790+2076A>G
ACVR1 transcript variant 6 NM_001347666.1:c.790+2076= NM_001347666.1:c.790+2076A>G
ACVR1 transcript variant 7 NM_001347667.2:c.790+2076= NM_001347667.2:c.790+2076A>G
ACVR1 transcript variant X1 XM_005246939.1:c.790+2076= XM_005246939.1:c.790+2076A>G
ACVR1 transcript variant X2 XM_005246940.1:c.790+2076= XM_005246940.1:c.790+2076A>G
ACVR1 transcript variant X2 XM_006712825.4:c.790+2076= XM_006712825.4:c.790+2076A>G
ACVR1 transcript variant X1 XM_011512108.3:c.790+2076= XM_011512108.3:c.790+2076A>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#.

65 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss14887820 Dec 05, 2003 (119)
2 PERLEGEN ss24308682 Sep 20, 2004 (123)
3 AFFY ss65947308 Nov 29, 2006 (127)
4 ILLUMINA ss66762996 Nov 29, 2006 (127)
5 ILLUMINA ss66888823 Nov 29, 2006 (127)
6 ILLUMINA ss66989952 Nov 29, 2006 (127)
7 PERLEGEN ss68832717 May 16, 2007 (127)
8 ILLUMINA ss70370214 May 16, 2007 (127)
9 ILLUMINA ss70484701 May 26, 2008 (130)
10 ILLUMINA ss71008774 May 16, 2007 (127)
11 ILLUMINA ss75775472 Dec 07, 2007 (129)
12 AFFY ss76714148 Dec 07, 2007 (129)
13 KRIBB_YJKIM ss84956527 Dec 16, 2007 (130)
14 BGI ss103615520 Dec 01, 2009 (131)
15 1000GENOMES ss110122688 Jan 24, 2009 (130)
16 ILLUMINA ss121332173 Dec 01, 2009 (131)
17 ILLUMINA ss152756611 Dec 01, 2009 (131)
18 ILLUMINA ss159129613 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss167343268 Jul 04, 2010 (132)
20 ILLUMINA ss169460098 Jul 04, 2010 (132)
21 ILLUMINA ss170216026 Jul 04, 2010 (132)
22 1000GENOMES ss231433043 Jul 14, 2010 (132)
23 1000GENOMES ss238927207 Jul 15, 2010 (132)
24 GMI ss276749949 May 04, 2012 (137)
25 ILLUMINA ss536614410 Sep 08, 2015 (146)
26 TISHKOFF ss555981663 Apr 25, 2013 (138)
27 SSMP ss649624021 Apr 25, 2013 (138)
28 ILLUMINA ss825339825 Apr 01, 2015 (144)
29 ILLUMINA ss832642303 Jul 13, 2019 (153)
30 EVA-GONL ss977546148 Aug 21, 2014 (142)
31 1000GENOMES ss1300056538 Aug 21, 2014 (142)
32 HAMMER_LAB ss1397309467 Sep 08, 2015 (146)
33 DDI ss1428793030 Apr 01, 2015 (144)
34 EVA_GENOME_DK ss1579160288 Apr 01, 2015 (144)
35 EVA_DECODE ss1586980855 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1604948576 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1647942609 Apr 01, 2015 (144)
38 EVA_SVP ss1712502711 Apr 01, 2015 (144)
39 HAMMER_LAB ss1797780817 Sep 08, 2015 (146)
40 WEILL_CORNELL_DGM ss1920799771 Feb 12, 2016 (147)
41 JJLAB ss2020929592 Sep 14, 2016 (149)
42 USC_VALOUEV ss2148995331 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2235802752 Dec 20, 2016 (150)
44 TOPMED ss2402197815 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2624969573 Nov 08, 2017 (151)
46 GRF ss2703627992 Nov 08, 2017 (151)
47 GNOMAD ss2781751503 Nov 08, 2017 (151)
48 SWEGEN ss2990715152 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3024227077 Nov 08, 2017 (151)
50 TOPMED ss3327815343 Nov 08, 2017 (151)
51 CSHL ss3344562087 Nov 08, 2017 (151)
52 ILLUMINA ss3628201739 Oct 11, 2018 (152)
53 ILLUMINA ss3638296907 Oct 11, 2018 (152)
54 ILLUMINA ss3639152500 Oct 11, 2018 (152)
55 ILLUMINA ss3639589081 Oct 11, 2018 (152)
56 ILLUMINA ss3643263156 Oct 11, 2018 (152)
57 EGCUT_WGS ss3658577090 Jul 13, 2019 (153)
58 EVA_DECODE ss3705241040 Jul 13, 2019 (153)
59 ACPOP ss3729025349 Jul 13, 2019 (153)
60 EVA ss3757606043 Jul 13, 2019 (153)
61 KHV_HUMAN_GENOMES ss3801966665 Jul 13, 2019 (153)
62 EVA ss3827309329 Apr 25, 2020 (154)
63 HGDP ss3847638630 Apr 25, 2020 (154)
64 SGDP_PRJ ss3853783121 Apr 25, 2020 (154)
65 KRGDB ss3899391846 Apr 25, 2020 (154)
66 1000Genomes NC_000002.11 - 158624804 Oct 11, 2018 (152)
67 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 158624804 Oct 11, 2018 (152)
68 Chileans NC_000002.11 - 158624804 Apr 25, 2020 (154)
69 Genome-wide autozygosity in Daghestan NC_000002.10 - 158333050 Apr 25, 2020 (154)
70 Genetic variation in the Estonian population NC_000002.11 - 158624804 Oct 11, 2018 (152)
71 The Danish reference pan genome NC_000002.11 - 158624804 Apr 25, 2020 (154)
72 gnomAD - Genomes NC_000002.11 - 158624804 Jul 13, 2019 (153)
73 Genome of the Netherlands Release 5 NC_000002.11 - 158624804 Apr 25, 2020 (154)
74 HGDP-CEPH-db Supplement 1 NC_000002.10 - 158333050 Apr 25, 2020 (154)
75 HapMap NC_000002.12 - 157768292 Apr 25, 2020 (154)
76 KOREAN population from KRGDB NC_000002.11 - 158624804 Apr 25, 2020 (154)
77 Northern Sweden NC_000002.11 - 158624804 Jul 13, 2019 (153)
78 Qatari NC_000002.11 - 158624804 Apr 25, 2020 (154)
79 SGDP_PRJ NC_000002.11 - 158624804 Apr 25, 2020 (154)
80 Siberian NC_000002.11 - 158624804 Apr 25, 2020 (154)
81 TopMed NC_000002.12 - 157768292 Oct 11, 2018 (152)
82 UK 10K study - Twins NC_000002.11 - 158624804 Oct 11, 2018 (152)
83 A Vietnamese Genetic Variation Database NC_000002.11 - 158624804 Jul 13, 2019 (153)
84 dbGaP Population Frequency Project NC_000002.12 - 157768292 Apr 25, 2020 (154)
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)
rs17188975 Oct 07, 2004 (123)
rs61462564 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3639152500, ss3639589081 NC_000002.9:158450311:T:C NC_000002.12:157768291:T:C (self)
259367, 316522, ss110122688, ss167343268, ss276749949, ss825339825, ss1397309467, ss1586980855, ss1712502711, ss3643263156, ss3847638630 NC_000002.10:158333049:T:C NC_000002.12:157768291:T:C (self)
11099769, 6119505, 233901, 4315338, 5325227, 30329148, 2688815, 6569240, 2310214, 2841701, 5800101, 1511685, 6119505, 1327728, ss231433043, ss238927207, ss536614410, ss555981663, ss649624021, ss832642303, ss977546148, ss1300056538, ss1428793030, ss1579160288, ss1604948576, ss1647942609, ss1797780817, ss1920799771, ss2020929592, ss2148995331, ss2402197815, ss2624969573, ss2703627992, ss2781751503, ss2990715152, ss3344562087, ss3628201739, ss3638296907, ss3658577090, ss3729025349, ss3757606043, ss3827309329, ss3853783121, ss3899391846 NC_000002.11:158624803:T:C NC_000002.12:157768291:T:C (self)
1930291, 208578802, 720017130, ss2235802752, ss3024227077, ss3327815343, ss3705241040, ss3801966665 NC_000002.12:157768291:T:C NC_000002.12:157768291:T:C (self)
ss14887820, ss24308682, ss65947308, ss66762996, ss66888823, ss66989952, ss68832717, ss70370214, ss70484701, ss71008774, ss75775472, ss76714148, ss84956527, ss103615520, ss121332173, ss152756611, ss159129613, ss169460098, ss170216026 NT_005403.17:8834221:T:C NC_000002.12:157768291:T:C (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 rs10497189
PMID Title Author Year Journal
18854405 Variants in the ACVR1 gene are associated with AMH levels in women with polycystic ovary syndrome. Kevenaar ME et al. 2009 Human reproduction (Oxford, England)
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
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.post565+e32b82c