Skip to main page content
Accesskeys

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.

rs10497189

Current Build 153

Released July 9, 2019

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=0.07213 (9057/125568, TOPMED)
C=0.0721 (2264/31392, GnomAD)
C=0.043 (216/5008, 1000G) (+ 5 more)
C=0.089 (397/4480, Estonian)
C=0.108 (415/3854, ALSPAC)
C=0.100 (371/3708, TWINSUK)
C=0.17 (102/600, NorthernSweden)
C=0.04 (8/216, Vietnamese)
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. N/A Intron Variant
ACVR1 transcript variant 2 NM_001111067.3:c. N/A Intron Variant
ACVR1 transcript variant 3 NM_001347663.1:c. N/A Intron Variant
ACVR1 transcript variant 4 NM_001347664.1:c. N/A Intron Variant
ACVR1 transcript variant 5 NM_001347665.1:c. N/A Intron Variant
ACVR1 transcript variant 6 NM_001347666.1:c. N/A Intron Variant
ACVR1 transcript variant 7 NM_001347667.2:c. N/A Intron Variant
ACVR1 transcript variant X2 XM_006712825.4:c. N/A Intron Variant
ACVR1 transcript variant X1 XM_011512108.3:c. 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
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=0.92787 C=0.07213
gnomAD - Genomes Global Study-wide 31392 T=0.9279 C=0.0721
gnomAD - Genomes European Sub 18896 T=0.9036 C=0.0964
gnomAD - Genomes African Sub 8714 T=0.977 C=0.023
gnomAD - Genomes East Asian Sub 1556 T=0.943 C=0.057
gnomAD - Genomes Other Sub 1088 T=0.925 C=0.075
gnomAD - Genomes American Sub 848 T=0.95 C=0.05
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.91 C=0.09
1000Genomes Global Study-wide 5008 T=0.957 C=0.043
1000Genomes African Sub 1322 T=0.995 C=0.005
1000Genomes East Asian Sub 1008 T=0.955 C=0.045
1000Genomes Europe Sub 1006 T=0.918 C=0.082
1000Genomes South Asian Sub 978 T=0.94 C=0.06
1000Genomes American Sub 694 T=0.97 C=0.03
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.911 C=0.089
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.892 C=0.108
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.900 C=0.100
Northern Sweden ACPOP Study-wide 600 T=0.83 C=0.17
A Vietnamese Genetic Variation Database Global Study-wide 216 T=0.96 C=0.04
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 Note
GRCh38.p12 chr 2 NC_000002.12:g.157768292= NC_000002.12:g.15776829...

NC_000002.12:g.157768292T>C

GRCh37.p13 chr 2 NC_000002.11:g.158624804= NC_000002.11:g.15862480...

NC_000002.11:g.158624804T>C

ACVR1 RefSeqGene NG_008004.1:g.111820= NG_008004.1:g.111820A>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#.

61 SubSNP, 8 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 1000Genomes NC_000002.11 - 158624804 Oct 11, 2018 (152)
63 The Avon Longitudinal Study of Parents and Children NC_000002.11 - 158624804 Oct 11, 2018 (152)
64 Genetic variation in the Estonian population NC_000002.11 - 158624804 Oct 11, 2018 (152)
65 gnomAD - Genomes NC_000002.11 - 158624804 Jul 13, 2019 (153)
66 Northern Sweden NC_000002.11 - 158624804 Jul 13, 2019 (153)
67 TopMed NC_000002.12 - 157768292 Oct 11, 2018 (152)
68 UK 10K study - Twins NC_000002.11 - 158624804 Oct 11, 2018 (152)
69 A Vietnamese Genetic Variation Database NC_000002.11 - 158624804 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)
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)
ss110122688, ss167343268, ss276749949, ss825339825, ss1397309467, ss1586980855, ss1712502711, ss3643263156 NC_000002.10:158333049:T:C NC_000002.12:157768291:T:C (self)
11099769, 6119505, 4315338, 30329148, 2310214, 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 NC_000002.11:158624803:T:C NC_000002.12:157768291:T:C (self)
208578802, 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

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.post246+3cda961