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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.

rs185832993

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:102949108 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000064 (17/264690, TOPMED)
A=0.000307 (77/251000, GnomAD_exome)
A=0.000220 (42/191078, ALFA) (+ 10 more)
A=0.000285 (40/140180, GnomAD)
A=0.000305 (37/121122, ExAC)
A=0.00005 (4/78698, PAGE_STUDY)
A=0.00004 (1/28258, 14KJPN)
A=0.0003 (2/6404, 1000G_30x)
A=0.0004 (2/5008, 1000G)
A=0.0027 (12/4480, Estonian)
A=0.0000 (0/3854, ALSPAC)
A=0.0003 (1/3708, TWINSUK)
A=0.002 (1/534, MGP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MMP13 : Missense Variant
Publications
0 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 207096 G=0.999792 A=0.000208
European Sub 173720 G=0.999776 A=0.000224
African Sub 9706 G=0.9999 A=0.0001
African Others Sub 360 G=1.000 A=0.000
African American Sub 9346 G=0.9999 A=0.0001
Asian Sub 6288 G=1.0000 A=0.0000
East Asian Sub 4466 G=1.0000 A=0.0000
Other Asian Sub 1822 G=1.0000 A=0.0000
Latin American 1 Sub 796 G=1.000 A=0.000
Latin American 2 Sub 968 G=1.000 A=0.000
South Asian Sub 274 G=1.000 A=0.000
Other Sub 15344 G=0.99980 A=0.00020


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=0.999936 A=0.000064
gnomAD - Exomes Global Study-wide 251000 G=0.999693 A=0.000307
gnomAD - Exomes European Sub 135024 G=0.999489 A=0.000511
gnomAD - Exomes Asian Sub 48988 G=0.99996 A=0.00004
gnomAD - Exomes American Sub 34538 G=0.99997 A=0.00003
gnomAD - Exomes African Sub 16250 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10074 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6126 G=0.9992 A=0.0008
Allele Frequency Aggregator Total Global 191078 G=0.999780 A=0.000220
Allele Frequency Aggregator European Sub 163960 G=0.999762 A=0.000238
Allele Frequency Aggregator Other Sub 13918 G=0.99978 A=0.00022
Allele Frequency Aggregator Asian Sub 6288 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 4874 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 968 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 796 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 274 G=1.000 A=0.000
gnomAD - Genomes Global Study-wide 140180 G=0.999715 A=0.000285
gnomAD - Genomes European Sub 75920 G=0.99953 A=0.00047
gnomAD - Genomes African Sub 42020 G=0.99995 A=0.00005
gnomAD - Genomes American Sub 13644 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3124 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=0.9991 A=0.0009
ExAC Global Study-wide 121122 G=0.999695 A=0.000305
ExAC Europe Sub 73210 G=0.99951 A=0.00049
ExAC Asian Sub 25124 G=1.00000 A=0.00000
ExAC American Sub 11488 G=0.99991 A=0.00009
ExAC African Sub 10392 G=1.00000 A=0.00000
ExAC Other Sub 908 G=1.000 A=0.000
The PAGE Study Global Study-wide 78698 G=0.99995 A=0.00005
The PAGE Study AfricanAmerican Sub 32516 G=0.99997 A=0.00003
The PAGE Study Mexican Sub 10808 G=1.00000 A=0.00000
The PAGE Study Asian Sub 8318 G=0.9998 A=0.0002
The PAGE Study PuertoRican Sub 7918 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4534 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4230 G=0.9998 A=0.0002
The PAGE Study Dominican Sub 3828 G=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1258 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
14KJPN JAPANESE Study-wide 28258 G=0.99996 A=0.00004
1000Genomes_30x Global Study-wide 6404 G=0.9997 A=0.0003
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9984 A=0.0016
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9996 A=0.0004
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9980 A=0.0020
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9973 A=0.0027
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=1.0000 A=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9997 A=0.0003
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.998 A=0.002
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 11 NC_000011.10:g.102949108G>A
GRCh37.p13 chr 11 NC_000011.9:g.102819837G>A
MMP13 RefSeqGene NG_021404.1:g.11627C>T
GRCh37.p13 chr 11 fix patch HG305_PATCH NW_003871077.1:g.117342G>A
Gene: MMP13, matrix metallopeptidase 13 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MMP13 transcript NM_002427.4:c.968C>T T [ACG] > M [ATG] Coding Sequence Variant
collagenase 3 preproprotein NP_002418.1:p.Thr323Met T (Thr) > M (Met) Missense 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: A (allele ID: 317748 )
ClinVar Accession Disease Names Clinical Significance
RCV000334477.3 Metaphyseal anadysplasia Benign
RCV000394865.3 Spondyloepimetaphyseal dysplasia, Missouri type Uncertain-Significance
RCV001502970.4 not provided Likely-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
GRCh38.p14 chr 11 NC_000011.10:g.102949108= NC_000011.10:g.102949108G>A
GRCh37.p13 chr 11 NC_000011.9:g.102819837= NC_000011.9:g.102819837G>A
MMP13 RefSeqGene NG_021404.1:g.11627= NG_021404.1:g.11627C>T
MMP13 transcript NM_002427.4:c.968= NM_002427.4:c.968C>T
MMP13 transcript NM_002427.3:c.968= NM_002427.3:c.968C>T
GRCh37.p13 chr 11 fix patch HG305_PATCH NW_003871077.1:g.117342= NW_003871077.1:g.117342G>A
collagenase 3 preproprotein NP_002418.1:p.Thr323= NP_002418.1:p.Thr323Met
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#.

39 SubSNP, 13 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss462494817 Sep 17, 2011 (135)
2 1000GENOMES ss491027951 May 04, 2012 (137)
3 EXOME_CHIP ss491458266 May 04, 2012 (137)
4 1000GENOMES ss1342733626 Aug 21, 2014 (142)
5 EVA_UK10K_ALSPAC ss1627336495 Apr 09, 2015 (144)
6 EVA_UK10K_TWINSUK ss1670330528 Apr 09, 2015 (144)
7 EVA_EXAC ss1690608944 Apr 09, 2015 (144)
8 EVA_MGP ss1711306913 Apr 09, 2015 (144)
9 ILLUMINA ss1751991249 Sep 11, 2015 (146)
10 ILLUMINA ss1917865675 Feb 17, 2016 (147)
11 ILLUMINA ss1946321100 Feb 17, 2016 (147)
12 ILLUMINA ss1959380896 Feb 17, 2016 (147)
13 HUMAN_LONGEVITY ss2185218961 Dec 20, 2016 (150)
14 GNOMAD ss2739350702 Oct 12, 2018 (152)
15 GNOMAD ss2748728543 Oct 12, 2018 (152)
16 GNOMAD ss2903797353 Oct 12, 2018 (152)
17 SWEGEN ss3008688378 Oct 12, 2018 (152)
18 ILLUMINA ss3021370778 Oct 12, 2018 (152)
19 ILLUMINA ss3634472753 Oct 12, 2018 (152)
20 ILLUMINA ss3640180090 Oct 12, 2018 (152)
21 ILLUMINA ss3644573959 Oct 12, 2018 (152)
22 ILLUMINA ss3651737745 Oct 12, 2018 (152)
23 EGCUT_WGS ss3676010059 Jul 13, 2019 (153)
24 ILLUMINA ss3725271482 Jul 13, 2019 (153)
25 ILLUMINA ss3744386655 Jul 13, 2019 (153)
26 ILLUMINA ss3744773544 Jul 13, 2019 (153)
27 PAGE_CC ss3771648839 Jul 13, 2019 (153)
28 ILLUMINA ss3772273326 Jul 13, 2019 (153)
29 GNOMAD ss4241487569 Apr 26, 2021 (155)
30 TOPMED ss4897911380 Apr 26, 2021 (155)
31 EVA ss5237500251 Apr 26, 2021 (155)
32 1000G_HIGH_COVERAGE ss5288700754 Oct 16, 2022 (156)
33 EVA ss5401875376 Oct 16, 2022 (156)
34 1000G_HIGH_COVERAGE ss5585082605 Oct 16, 2022 (156)
35 TOMMO_GENOMICS ss5752005164 Oct 16, 2022 (156)
36 EVA ss5847645962 Oct 16, 2022 (156)
37 EVA ss5921422689 Oct 16, 2022 (156)
38 EVA ss5943280563 Oct 16, 2022 (156)
39 EVA ss5979369897 Oct 16, 2022 (156)
40 1000Genomes NC_000011.9 - 102819837 Oct 12, 2018 (152)
41 1000Genomes_30x NC_000011.10 - 102949108 Oct 16, 2022 (156)
42 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 102819837 Oct 12, 2018 (152)
43 Genetic variation in the Estonian population NC_000011.9 - 102819837 Oct 12, 2018 (152)
44 ExAC NC_000011.9 - 102819837 Oct 12, 2018 (152)
45 gnomAD - Genomes NC_000011.10 - 102949108 Apr 26, 2021 (155)
46 gnomAD - Exomes NC_000011.9 - 102819837 Jul 13, 2019 (153)
47 Medical Genome Project healthy controls from Spanish population NC_000011.9 - 102819837 Apr 26, 2020 (154)
48 The PAGE Study NC_000011.10 - 102949108 Jul 13, 2019 (153)
49 14KJPN NC_000011.10 - 102949108 Oct 16, 2022 (156)
50 TopMed NC_000011.10 - 102949108 Apr 26, 2021 (155)
51 UK 10K study - Twins NC_000011.9 - 102819837 Oct 12, 2018 (152)
52 ALFA NC_000011.10 - 102949108 Apr 26, 2021 (155)
53 ClinVar RCV000334477.3 Oct 16, 2022 (156)
54 ClinVar RCV000394865.3 Oct 16, 2022 (156)
55 ClinVar RCV001502970.4 Oct 16, 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
55306944, 30693124, 21748307, 882805, 8568421, 422673, 30693124, ss462494817, ss491027951, ss491458266, ss1342733626, ss1627336495, ss1670330528, ss1690608944, ss1711306913, ss1751991249, ss1917865675, ss1946321100, ss1959380896, ss2739350702, ss2748728543, ss2903797353, ss3008688378, ss3021370778, ss3634472753, ss3640180090, ss3644573959, ss3651737745, ss3676010059, ss3744386655, ss3744773544, ss3772273326, ss5237500251, ss5401875376, ss5847645962, ss5943280563, ss5979369897 NC_000011.9:102819836:G:A NC_000011.10:102949107:G:A (self)
RCV000334477.3, RCV000394865.3, RCV001502970.4, 72608540, 390270090, 870308, 85842268, 113457036, 5026898239, ss2185218961, ss3725271482, ss3771648839, ss4241487569, ss4897911380, ss5288700754, ss5585082605, ss5752005164, ss5921422689 NC_000011.10:102949107:G:A NC_000011.10:102949107:G:A (self)
Help

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

No publications for rs185832993

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.post761+d5e8e07