Name: rs2222293
Published: September 21, 2022
License: Open Access

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.

rs2222293

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr8:88312424 (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>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.025868 (6847/264690, TOPMED)
C=0.024969 (3502/140254, GnomAD)
C=0.00000 (0/28258, 14KJPN) (+ 17 more)
C=0.00000 (0/16760, 8.3KJPN)
C=0.01401 (158/11274, ALFA)
C=0.0320 (205/6404, 1000G_30x)
C=0.0304 (152/5008, 1000G)
C=0.0040 (18/4480, Estonian)
C=0.0101 (39/3854, ALSPAC)
C=0.0105 (39/3708, TWINSUK)
C=0.0007 (2/2930, KOREAN)
C=0.0000 (0/1832, Korea1K)
C=0.0463 (72/1556, HapMap)
C=0.008 (8/998, GoNL)
C=0.000 (0/600, NorthernSweden)
C=0.002 (1/558, SGDP_PRJ)
C=0.000 (0/216, Qatari)
C=0.000 (0/212, Vietnamese)
C=0.02 (1/56, Siberian)
C=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MMP16 : 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	11274	C=0.01401	G=0.00000, T=0.98599
European	Sub	8704	C=0.0057	G=0.0000, T=0.9943
African	Sub	1354	C=0.0672	G=0.0000, T=0.9328
African Others	Sub	42	C=0.12	G=0.00, T=0.88
African American	Sub	1312	C=0.0655	G=0.0000, T=0.9345
Asian	Sub	56	C=0.00	G=0.00, T=1.00
East Asian	Sub	20	C=0.00	G=0.00, T=1.00
Other Asian	Sub	36	C=0.00	G=0.00, T=1.00
Latin American 1	Sub	76	C=0.05	G=0.00, T=0.95
Latin American 2	Sub	150	C=0.007	G=0.000, T=0.993
South Asian	Sub	16	C=0.00	G=0.00, T=1.00
Other	Sub	918	C=0.013	G=0.000, T=0.987

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
TopMed	Global	Study-wide	264690	C=0.025868	T=0.974132
gnomAD - Genomes	Global	Study-wide	140254	C=0.024969	T=0.975031
gnomAD - Genomes	European	Sub	75972	C=0.00842	T=0.99158
gnomAD - Genomes	African	Sub	42018	C=0.06283	T=0.93717
gnomAD - Genomes	American	Sub	13658	C=0.01062	T=0.98938
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.0072	T=0.9928
gnomAD - Genomes	East Asian	Sub	3132	C=0.0000	T=1.0000
gnomAD - Genomes	Other	Sub	2150	C=0.0247	T=0.9753
14KJPN	JAPANESE	Study-wide	28258	C=0.00000	T=1.00000
8.3KJPN	JAPANESE	Study-wide	16760	C=0.00000	T=1.00000
Allele Frequency Aggregator	Total	Global	11274	C=0.01401	G=0.00000, T=0.98599
Allele Frequency Aggregator	European	Sub	8704	C=0.0057	G=0.0000, T=0.9943
Allele Frequency Aggregator	African	Sub	1354	C=0.0672	G=0.0000, T=0.9328
Allele Frequency Aggregator	Other	Sub	918	C=0.013	G=0.000, T=0.987
Allele Frequency Aggregator	Latin American 2	Sub	150	C=0.007	G=0.000, T=0.993
Allele Frequency Aggregator	Latin American 1	Sub	76	C=0.05	G=0.00, T=0.95
Allele Frequency Aggregator	Asian	Sub	56	C=0.00	G=0.00, T=1.00
Allele Frequency Aggregator	South Asian	Sub	16	C=0.00	G=0.00, T=1.00
1000Genomes_30x	Global	Study-wide	6404	C=0.0320	T=0.9680
1000Genomes_30x	African	Sub	1786	C=0.0974	T=0.9026
1000Genomes_30x	Europe	Sub	1266	C=0.0095	T=0.9905
1000Genomes_30x	South Asian	Sub	1202	C=0.0067	T=0.9933
1000Genomes_30x	East Asian	Sub	1170	C=0.0000	T=1.0000
1000Genomes_30x	American	Sub	980	C=0.011	T=0.989
1000Genomes	Global	Study-wide	5008	C=0.0304	T=0.9696
1000Genomes	African	Sub	1322	C=0.0968	T=0.9032
1000Genomes	East Asian	Sub	1008	C=0.0000	T=1.0000
1000Genomes	Europe	Sub	1006	C=0.0099	T=0.9901
1000Genomes	South Asian	Sub	978	C=0.007	T=0.993
1000Genomes	American	Sub	694	C=0.010	T=0.990
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.0040	T=0.9960
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.0101	T=0.9899
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.0105	T=0.9895
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0007	A=0.0000, T=0.9993
Korean Genome Project	KOREAN	Study-wide	1832	C=0.0000	T=1.0000
HapMap	Global	Study-wide	1556	C=0.0463	T=0.9537
HapMap	African	Sub	692	C=0.082	T=0.918
HapMap	American	Sub	600	C=0.017	T=0.983
HapMap	Europe	Sub	174	C=0.029	T=0.971
HapMap	Asian	Sub	90	C=0.00	T=1.00
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.008	T=0.992
Northern Sweden	ACPOP	Study-wide	600	C=0.000	T=1.000
SGDP_PRJ	Global	Study-wide	558	C=0.002	T=0.998
Qatari	Global	Study-wide	216	C=0.000	T=1.000
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.000	T=1.000
Siberian	Global	Study-wide	56	C=0.02	T=0.98
The Danish reference pan genome	Danish	Study-wide	40	C=0.00	T=1.00

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 8	NC_000008.11:g.88312424C>A
GRCh38.p14 chr 8	NC_000008.11:g.88312424C>G
GRCh38.p14 chr 8	NC_000008.11:g.88312424C>T
GRCh37.p13 chr 8	NC_000008.10:g.89324653C>A
GRCh37.p13 chr 8	NC_000008.10:g.89324653C>G
GRCh37.p13 chr 8	NC_000008.10:g.89324653C>T

Gene: MMP16, matrix metallopeptidase 16 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MMP16 transcript	NM_005941.5:c.132+14651G>T	N/A	Intron Variant
MMP16 transcript variant X1	XM_024447154.2:c.	N/A	Genic Upstream Transcript Variant

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

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=	A	G	T
GRCh38.p14 chr 8	NC_000008.11:g.88312424=	NC_000008.11:g.88312424C>A	NC_000008.11:g.88312424C>G	NC_000008.11:g.88312424C>T
GRCh37.p13 chr 8	NC_000008.10:g.89324653=	NC_000008.10:g.89324653C>A	NC_000008.10:g.89324653C>G	NC_000008.10:g.89324653C>T
MMP16 transcript	NM_005941.4:c.132+14651=	NM_005941.4:c.132+14651G>T	NM_005941.4:c.132+14651G>C	NM_005941.4:c.132+14651G>A
MMP16 transcript	NM_005941.5:c.132+14651=	NM_005941.5:c.132+14651G>T	NM_005941.5:c.132+14651G>C	NM_005941.5:c.132+14651G>A
MMP16 transcript variant X1	XM_005250921.1:c.132+14651=	XM_005250921.1:c.132+14651G>T	XM_005250921.1:c.132+14651G>C	XM_005250921.1:c.132+14651G>A

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#.

86 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss3166004	Jun 15, 2001 (96)
2	SC_JCM	ss5826440	Feb 20, 2003 (123)
3	WI_SSAHASNP	ss11938757	Jul 11, 2003 (123)
4	CSHL-HAPMAP	ss17975589	Feb 27, 2004 (123)
5	SSAHASNP	ss22659387	Apr 05, 2004 (123)
6	EGP_SNPS	ss37042930	May 24, 2005 (125)
7	ABI	ss43252603	Mar 13, 2006 (126)
8	AFFY	ss66289707	Dec 01, 2006 (127)
9	AFFY	ss75953414	Dec 06, 2007 (129)
10	HGSV	ss78506665	Dec 06, 2007 (129)
11	KRIBB_YJKIM	ss81728721	Dec 15, 2007 (130)
12	BCMHGSC_JDW	ss93924552	Mar 25, 2008 (129)
13	BGI	ss105631605	Feb 06, 2009 (130)
14	1000GENOMES	ss108195362	Jan 23, 2009 (130)
15	1000GENOMES	ss113361671	Jan 25, 2009 (130)
16	ILLUMINA-UK	ss116056918	Feb 14, 2009 (130)
17	ENSEMBL	ss134308799	Dec 01, 2009 (131)
18	ENSEMBL	ss143619384	Dec 01, 2009 (131)
19	GMI	ss156612003	Dec 01, 2009 (131)
20	COMPLETE_GENOMICS	ss162576426	Jul 04, 2010 (132)
21	COMPLETE_GENOMICS	ss165215390	Jul 04, 2010 (132)
22	COMPLETE_GENOMICS	ss166858317	Jul 04, 2010 (132)
23	AFFY	ss169609109	Jul 04, 2010 (132)
24	BUSHMAN	ss199448578	Jul 04, 2010 (132)
25	BCM-HGSC-SUB	ss208525308	Jul 04, 2010 (132)
26	1000GENOMES	ss223834476	Jul 14, 2010 (132)
27	1000GENOMES	ss234528130	Jul 15, 2010 (132)
28	1000GENOMES	ss241363995	Jul 15, 2010 (132)
29	BL	ss254482453	May 09, 2011 (134)
30	GMI	ss279902507	May 04, 2012 (137)
31	GMI	ss285882296	Apr 25, 2013 (138)
32	PJP	ss294124816	May 09, 2011 (134)
33	ILLUMINA	ss533465436	Sep 08, 2015 (146)
34	TISHKOFF	ss560898923	Apr 25, 2013 (138)
35	SSMP	ss655338365	Apr 25, 2013 (138)
36	EVA-GONL	ss985773497	Aug 21, 2014 (142)
37	JMKIDD_LAB	ss1075709674	Aug 21, 2014 (142)
38	1000GENOMES	ss1330840828	Aug 21, 2014 (142)
39	DDI	ss1431587218	Apr 01, 2015 (144)
40	EVA_GENOME_DK	ss1582780381	Apr 01, 2015 (144)
41	EVA_DECODE	ss1595378025	Apr 01, 2015 (144)
42	EVA_UK10K_ALSPAC	ss1621155405	Apr 01, 2015 (144)
43	EVA_UK10K_TWINSUK	ss1664149438	Apr 01, 2015 (144)
44	EVA_SVP	ss1713052059	Apr 01, 2015 (144)
45	HAMMER_LAB	ss1805641343	Sep 08, 2015 (146)
46	WEILL_CORNELL_DGM	ss1929055416	Feb 12, 2016 (147)
47	GENOMED	ss1971033010	Jul 19, 2016 (147)
48	JJLAB	ss2025233080	Sep 14, 2016 (149)
49	USC_VALOUEV	ss2153457295	Dec 20, 2016 (150)
50	HUMAN_LONGEVITY	ss2305169685	Dec 20, 2016 (150)
51	SYSTEMSBIOZJU	ss2627091864	Nov 08, 2017 (151)
52	GRF	ss2709232843	Nov 08, 2017 (151)
53	GNOMAD	ss2869615825	Nov 08, 2017 (151)
54	SWEGEN	ss3003574652	Nov 08, 2017 (151)
55	BIOINF_KMB_FNS_UNIBA	ss3026401298	Nov 08, 2017 (151)
56	CSHL	ss3348289503	Nov 08, 2017 (151)
57	ILLUMINA	ss3630105665	Oct 12, 2018 (152)
58	URBANLAB	ss3648963282	Oct 12, 2018 (152)
59	EGCUT_WGS	ss3671272118	Jul 13, 2019 (153)
60	EVA_DECODE	ss3722489400	Jul 13, 2019 (153)
61	ACPOP	ss3735873527	Jul 13, 2019 (153)
62	EVA	ss3768291137	Jul 13, 2019 (153)
63	PACBIO	ss3786208768	Jul 13, 2019 (153)
64	PACBIO	ss3791453769	Jul 13, 2019 (153)
65	PACBIO	ss3796335181	Jul 13, 2019 (153)
66	KHV_HUMAN_GENOMES	ss3811453890	Jul 13, 2019 (153)
67	EVA	ss3831282385	Apr 26, 2020 (154)
68	EVA	ss3839148168	Apr 26, 2020 (154)
69	EVA	ss3844608635	Apr 26, 2020 (154)
70	SGDP_PRJ	ss3870437774	Apr 26, 2020 (154)
71	KRGDB	ss3917988016	Apr 26, 2020 (154)
72	KOGIC	ss3964331488	Apr 26, 2020 (154)
73	TOPMED	ss4794795940	Apr 26, 2021 (155)
74	TOMMO_GENOMICS	ss5189800773	Apr 26, 2021 (155)
75	1000G_HIGH_COVERAGE	ss5278006138	Oct 16, 2022 (156)
76	EVA	ss5382732599	Oct 16, 2022 (156)
77	HUGCELL_USP	ss5474478504	Oct 16, 2022 (156)
78	EVA	ss5509451131	Oct 16, 2022 (156)
79	1000G_HIGH_COVERAGE	ss5568837151	Oct 16, 2022 (156)
80	SANFORD_IMAGENETICS	ss5645878967	Oct 16, 2022 (156)
81	TOMMO_GENOMICS	ss5732182779	Oct 16, 2022 (156)
82	YY_MCH	ss5809913107	Oct 16, 2022 (156)
83	EVA	ss5830864679	Oct 16, 2022 (156)
84	EVA	ss5856467726	Oct 16, 2022 (156)
85	EVA	ss5889951184	Oct 16, 2022 (156)
86	EVA	ss5975106946	Oct 16, 2022 (156)
87	1000Genomes	NC_000008.10 - 89324653	Oct 12, 2018 (152)
88	1000Genomes_30x	NC_000008.11 - 88312424	Oct 16, 2022 (156)
89	The Avon Longitudinal Study of Parents and Children	NC_000008.10 - 89324653	Oct 12, 2018 (152)
90	Genetic variation in the Estonian population	NC_000008.10 - 89324653	Oct 12, 2018 (152)
91	The Danish reference pan genome	NC_000008.10 - 89324653	Apr 26, 2020 (154)
92	gnomAD - Genomes	NC_000008.11 - 88312424	Apr 26, 2021 (155)
93	Genome of the Netherlands Release 5	NC_000008.10 - 89324653	Apr 26, 2020 (154)
94	HapMap	NC_000008.11 - 88312424	Apr 26, 2020 (154)
95	KOREAN population from KRGDB	NC_000008.10 - 89324653	Apr 26, 2020 (154)
96	Korean Genome Project	NC_000008.11 - 88312424	Apr 26, 2020 (154)
97	Northern Sweden	NC_000008.10 - 89324653	Jul 13, 2019 (153)
98	Qatari	NC_000008.10 - 89324653	Apr 26, 2020 (154)
99	SGDP_PRJ	NC_000008.10 - 89324653	Apr 26, 2020 (154)
100	Siberian	NC_000008.10 - 89324653	Apr 26, 2020 (154)
101	8.3KJPN	NC_000008.10 - 89324653	Apr 26, 2021 (155)
102	14KJPN	NC_000008.11 - 88312424	Oct 16, 2022 (156)
103	TopMed	NC_000008.11 - 88312424	Apr 26, 2021 (155)
104	UK 10K study - Twins	NC_000008.10 - 89324653	Oct 12, 2018 (152)
105	A Vietnamese Genetic Variation Database	NC_000008.10 - 89324653	Jul 13, 2019 (153)
106	ALFA	NC_000008.11 - 88312424	Apr 26, 2021 (155)

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)
rs4370581	Oct 08, 2004 (123)
rs58895857	Feb 27, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
25165410, ss3917988016	NC_000008.10:89324652:C:A	NC_000008.11:88312423:C:A	(self)
3083310520	NC_000008.11:88312423:C:G	NC_000008.11:88312423:C:G	(self)
ss66289707, ss75953414, ss78506665, ss93924552, ss108195362, ss113361671, ss116056918, ss162576426, ss165215390, ss166858317, ss169609109, ss199448578, ss208525308, ss254482453, ss279902507, ss285882296, ss294124816, ss1595378025, ss1713052059	NC_000008.9:89393768:C:T	NC_000008.11:88312423:C:T	(self)
43000560, 23913377, 17010366, 8945319, 10675753, 25165410, 9158392, 11097346, 22454754, 5973649, 47770080, 23913377, 5318290, ss223834476, ss234528130, ss241363995, ss533465436, ss560898923, ss655338365, ss985773497, ss1075709674, ss1330840828, ss1431587218, ss1582780381, ss1621155405, ss1664149438, ss1805641343, ss1929055416, ss1971033010, ss2025233080, ss2153457295, ss2627091864, ss2709232843, ss2869615825, ss3003574652, ss3348289503, ss3630105665, ss3671272118, ss3735873527, ss3768291137, ss3786208768, ss3791453769, ss3796335181, ss3831282385, ss3839148168, ss3870437774, ss3917988016, ss5189800773, ss5382732599, ss5509451131, ss5645878967, ss5830864679, ss5975106946	NC_000008.10:89324652:C:T	NC_000008.11:88312423:C:T	(self)
56363086, 303269484, 3669194, 20709489, 66019883, 632173500, 3083310520, ss2305169685, ss3026401298, ss3648963282, ss3722489400, ss3811453890, ss3844608635, ss3964331488, ss4794795940, ss5278006138, ss5474478504, ss5568837151, ss5732182779, ss5809913107, ss5856467726, ss5889951184	NC_000008.11:88312423:C:T	NC_000008.11:88312423:C:T	(self)
ss11938757	NT_008046.13:2542765:C:T	NC_000008.11:88312423:C:T	(self)
ss17975589, ss22659387	NT_008046.14:2542765:C:T	NC_000008.11:88312423:C:T	(self)
ss3166004, ss5826440, ss37042930, ss43252603, ss81728721, ss105631605, ss134308799, ss143619384, ss156612003	NT_008046.16:2598201:C:T	NC_000008.11:88312423:C:T	(self)

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

No publications for rs2222293

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
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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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2222293