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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs17099014

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:102611863 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.008085 (2140/264690, TOPMED)
T=0.001782 (448/251446, GnomAD_exome)
T=0.000869 (177/203586, ALFA) (+ 7 more)
T=0.007236 (1015/140280, GnomAD)
T=0.002119 (257/121284, ExAC)
T=0.01160 (913/78700, PAGE_STUDY)
T=0.00623 (81/13004, GO-ESP)
T=0.0086 (55/6404, 1000G_30x)
T=0.0076 (38/5008, 1000G)
T=0.010 (8/796, HapMap)
Clinical Significance
Reported in ClinVar
Gene : Consequence
MMP20 : Missense Variant
LOC101928477 : Intron 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 219988 C=0.998554 T=0.001446
European Sub 181524 C=0.999950 T=0.000050
African Sub 11618 C=0.97650 T=0.02350
African Others Sub 398 C=0.970 T=0.030
African American Sub 11220 C=0.97674 T=0.02326
Asian Sub 6402 C=1.0000 T=0.0000
East Asian Sub 4520 C=1.0000 T=0.0000
Other Asian Sub 1882 C=1.0000 T=0.0000
Latin American 1 Sub 870 C=0.992 T=0.008
Latin American 2 Sub 1118 C=0.9991 T=0.0009
South Asian Sub 292 C=1.000 T=0.000
Other Sub 18164 C=0.99846 T=0.00154


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 C=0.991915 T=0.008085
gnomAD - Exomes Global Study-wide 251446 C=0.998218 T=0.001782
gnomAD - Exomes European Sub 135382 C=0.999985 T=0.000015
gnomAD - Exomes Asian Sub 49004 C=0.99992 T=0.00008
gnomAD - Exomes American Sub 34588 C=0.99867 T=0.00133
gnomAD - Exomes African Sub 16256 C=0.97589 T=0.02411
gnomAD - Exomes Ashkenazi Jewish Sub 10080 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6136 C=0.9993 T=0.0007
Allele Frequency Aggregator Total Global 203586 C=0.999131 T=0.000869
Allele Frequency Aggregator European Sub 171390 C=0.999953 T=0.000047
Allele Frequency Aggregator Other Sub 16730 C=0.99880 T=0.00120
Allele Frequency Aggregator African Sub 6784 C=0.9792 T=0.0208
Allele Frequency Aggregator Asian Sub 6402 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 1118 C=0.9991 T=0.0009
Allele Frequency Aggregator Latin American 1 Sub 870 C=0.992 T=0.008
Allele Frequency Aggregator South Asian Sub 292 C=1.000 T=0.000
gnomAD - Genomes Global Study-wide 140280 C=0.992764 T=0.007236
gnomAD - Genomes European Sub 75958 C=0.99992 T=0.00008
gnomAD - Genomes African Sub 42052 C=0.97686 T=0.02314
gnomAD - Genomes American Sub 13664 C=0.99795 T=0.00205
gnomAD - Genomes Ashkenazi Jewish Sub 3320 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3132 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=0.9963 T=0.0037
ExAC Global Study-wide 121284 C=0.997881 T=0.002119
ExAC Europe Sub 73264 C=0.99999 T=0.00001
ExAC Asian Sub 25152 C=0.99992 T=0.00008
ExAC American Sub 11566 C=0.99888 T=0.00112
ExAC African Sub 10396 C=0.97691 T=0.02309
ExAC Other Sub 906 C=0.999 T=0.001
The PAGE Study Global Study-wide 78700 C=0.98840 T=0.01160
The PAGE Study AfricanAmerican Sub 32516 C=0.97663 T=0.02337
The PAGE Study Mexican Sub 10808 C=0.99870 T=0.00130
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=0.9939 T=0.0061
The PAGE Study NativeHawaiian Sub 4534 C=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 C=0.9974 T=0.0026
The PAGE Study Dominican Sub 3828 C=0.9830 T=0.0170
The PAGE Study CentralAmerican Sub 2450 C=0.9967 T=0.0033
The PAGE Study SouthAmerican Sub 1982 C=0.9985 T=0.0015
The PAGE Study NativeAmerican Sub 1260 C=0.9968 T=0.0032
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13004 C=0.99377 T=0.00623
GO Exome Sequencing Project European American Sub 8598 C=1.0000 T=0.0000
GO Exome Sequencing Project African American Sub 4406 C=0.9816 T=0.0184
1000Genomes_30x Global Study-wide 6404 C=0.9914 T=0.0086
1000Genomes_30x African Sub 1786 C=0.9709 T=0.0291
1000Genomes_30x Europe Sub 1266 C=0.9984 T=0.0016
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=0.999 T=0.001
1000Genomes Global Study-wide 5008 C=0.9924 T=0.0076
1000Genomes African Sub 1322 C=0.9728 T=0.0272
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9990 T=0.0010
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=0.999 T=0.001
HapMap Global Study-wide 796 C=0.990 T=0.010
HapMap African Sub 402 C=0.988 T=0.012
HapMap American Sub 310 C=0.990 T=0.010
HapMap Asian Sub 84 C=1.00 T=0.00
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.102611863C>T
GRCh37.p13 chr 11 NC_000011.9:g.102482594C>T
MMP20 RefSeqGene NG_012151.1:g.18470G>A
Gene: MMP20, matrix metallopeptidase 20 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MMP20 transcript NM_004771.4:c.415G>A D [GAC] > N [AAC] Coding Sequence Variant
matrix metalloproteinase-20 preproprotein NP_004762.2:p.Asp139Asn D (Asp) > N (Asn) Missense Variant
Gene: LOC101928477, uncharacterized LOC101928477 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
LOC101928477 transcript variant X4 XR_001748340.2:n. N/A Intron Variant
LOC101928477 transcript variant X5 XR_001748341.2:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X2 XR_007062866.1:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X6 XR_007062867.1:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X1 XR_947957.3:n. N/A Genic Upstream Transcript Variant
LOC101928477 transcript variant X3 XR_947958.3:n. N/A Genic 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: 312063 )
ClinVar Accession Disease Names Clinical Significance
RCV000380309.3 Amelogenesis imperfecta hypomaturation type 2A2 Likely-Benign
RCV000969269.3 not provided 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 C= T
GRCh38.p14 chr 11 NC_000011.10:g.102611863= NC_000011.10:g.102611863C>T
GRCh37.p13 chr 11 NC_000011.9:g.102482594= NC_000011.9:g.102482594C>T
MMP20 RefSeqGene NG_012151.1:g.18470= NG_012151.1:g.18470G>A
MMP20 transcript NM_004771.4:c.415= NM_004771.4:c.415G>A
MMP20 transcript NM_004771.3:c.415= NM_004771.3:c.415G>A
matrix metalloproteinase-20 preproprotein NP_004762.2:p.Asp139= NP_004762.2:p.Asp139Asn
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#.

60 SubSNP, 10 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EGP_SNPS ss28446804 Sep 20, 2004 (123)
2 PERLEGEN ss69327104 May 18, 2007 (127)
3 AFFY ss74817261 Aug 16, 2007 (128)
4 ILLUMINA ss74911366 Dec 07, 2007 (129)
5 AFFY ss76661840 Dec 07, 2007 (129)
6 CANCER-GENOME ss86349792 Mar 23, 2008 (129)
7 KRIBB_YJKIM ss119873851 Dec 01, 2009 (131)
8 ILLUMINA ss172744154 Jul 04, 2010 (132)
9 1000GENOMES ss336950215 May 09, 2011 (134)
10 NHLBI-ESP ss342338914 May 09, 2011 (134)
11 1000GENOMES ss491027738 May 04, 2012 (137)
12 EXOME_CHIP ss491458109 May 04, 2012 (137)
13 ILLUMINA ss534822873 Sep 08, 2015 (146)
14 ILLUMINA ss780903188 Sep 08, 2015 (146)
15 ILLUMINA ss783590405 Sep 08, 2015 (146)
16 JMKIDD_LAB ss1067527566 Aug 21, 2014 (142)
17 JMKIDD_LAB ss1077997912 Aug 21, 2014 (142)
18 1000GENOMES ss1342723091 Aug 21, 2014 (142)
19 EVA_EXAC ss1690605780 Apr 01, 2015 (144)
20 ILLUMINA ss1751990943 Sep 08, 2015 (146)
21 ILLUMINA ss1917865535 Feb 12, 2016 (147)
22 ILLUMINA ss1946320881 Feb 12, 2016 (147)
23 ILLUMINA ss1959380478 Feb 12, 2016 (147)
24 HUMAN_LONGEVITY ss2185197924 Dec 20, 2016 (150)
25 ILLUMINA ss2632880241 Nov 08, 2017 (151)
26 GNOMAD ss2739346117 Nov 08, 2017 (151)
27 GNOMAD ss2748727095 Nov 08, 2017 (151)
28 GNOMAD ss2903769004 Nov 08, 2017 (151)
29 AFFY ss2984954789 Nov 08, 2017 (151)
30 ILLUMINA ss3021370343 Nov 08, 2017 (151)
31 ILLUMINA ss3625608199 Oct 12, 2018 (152)
32 ILLUMINA ss3626737368 Oct 12, 2018 (152)
33 ILLUMINA ss3626737369 Oct 12, 2018 (152)
34 ILLUMINA ss3634472469 Oct 12, 2018 (152)
35 ILLUMINA ss3637927094 Oct 12, 2018 (152)
36 ILLUMINA ss3640179806 Oct 12, 2018 (152)
37 ILLUMINA ss3642923876 Oct 12, 2018 (152)
38 ILLUMINA ss3644573740 Oct 12, 2018 (152)
39 ILLUMINA ss3651737293 Oct 12, 2018 (152)
40 ILLUMINA ss3653727390 Oct 12, 2018 (152)
41 ILLUMINA ss3725271060 Jul 13, 2019 (153)
42 ILLUMINA ss3744386512 Jul 13, 2019 (153)
43 ILLUMINA ss3744773264 Jul 13, 2019 (153)
44 PAGE_CC ss3771648486 Jul 13, 2019 (153)
45 ILLUMINA ss3772273050 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3815069909 Jul 13, 2019 (153)
47 EVA ss3824665674 Apr 26, 2020 (154)
48 EVA ss3986542994 Apr 27, 2021 (155)
49 EVA ss4017555957 Apr 27, 2021 (155)
50 TOPMED ss4897823903 Apr 27, 2021 (155)
51 1000G_HIGH_COVERAGE ss5288691785 Oct 16, 2022 (156)
52 EVA ss5401859007 Oct 16, 2022 (156)
53 HUGCELL_USP ss5483701501 Oct 16, 2022 (156)
54 1000G_HIGH_COVERAGE ss5585069087 Oct 16, 2022 (156)
55 SANFORD_IMAGENETICS ss5624283912 Oct 16, 2022 (156)
56 SANFORD_IMAGENETICS ss5651953084 Oct 16, 2022 (156)
57 EVA ss5847645729 Oct 16, 2022 (156)
58 EVA ss5921412207 Oct 16, 2022 (156)
59 EVA ss5943275077 Oct 16, 2022 (156)
60 EVA ss5979369746 Oct 16, 2022 (156)
61 1000Genomes NC_000011.9 - 102482594 Oct 12, 2018 (152)
62 1000Genomes_30x NC_000011.10 - 102611863 Oct 16, 2022 (156)
63 ExAC NC_000011.9 - 102482594 Oct 12, 2018 (152)
64 gnomAD - Genomes NC_000011.10 - 102611863 Apr 27, 2021 (155)
65 gnomAD - Exomes NC_000011.9 - 102482594 Jul 13, 2019 (153)
66 GO Exome Sequencing Project NC_000011.9 - 102482594 Oct 12, 2018 (152)
67 HapMap NC_000011.10 - 102611863 Apr 26, 2020 (154)
68 The PAGE Study NC_000011.10 - 102611863 Jul 13, 2019 (153)
69 TopMed NC_000011.10 - 102611863 Apr 27, 2021 (155)
70 ALFA NC_000011.10 - 102611863 Apr 27, 2021 (155)
71 ClinVar RCV000380309.3 Oct 16, 2022 (156)
72 ClinVar RCV000969269.3 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).

Associated ID History Updated (Build)
rs52798131 Sep 21, 2007 (128)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3642923876 NC_000011.8:101987803:C:T NC_000011.10:102611862:C:T (self)
55296094, 879397, 8563462, 1123220, ss336950215, ss342338914, ss491027738, ss491458109, ss534822873, ss780903188, ss783590405, ss1067527566, ss1077997912, ss1342723091, ss1690605780, ss1751990943, ss1917865535, ss1946320881, ss1959380478, ss2632880241, ss2739346117, ss2748727095, ss2903769004, ss2984954789, ss3021370343, ss3625608199, ss3626737368, ss3626737369, ss3634472469, ss3637927094, ss3640179806, ss3644573740, ss3651737293, ss3653727390, ss3744386512, ss3744773264, ss3772273050, ss3824665674, ss3986542994, ss4017555957, ss5401859007, ss5624283912, ss5651953084, ss5847645729, ss5943275077, ss5979369746 NC_000011.9:102482593:C:T NC_000011.10:102611862:C:T (self)
RCV000380309.3, RCV000969269.3, 72595022, 390198403, 684771, 869955, 113369559, 573319299, ss2185197924, ss3725271060, ss3771648486, ss3815069909, ss4897823903, ss5288691785, ss5483701501, ss5585069087, ss5921412207 NC_000011.10:102611862:C:T NC_000011.10:102611862:C:T (self)
ss28446804, ss69327104, ss74817261, ss74911366, ss76661840, ss86349792, ss119873851, ss172744154 NT_033899.8:6045009:C:T NC_000011.10:102611862:C:T (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 rs17099014

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