Name: rs738790
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.

rs738790

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:23774630 (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: T>A / T>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.085050 (22512/264690, TOPMED)
T=0.075968 (10641/140072, GnomAD)
T=0.34513 (9752/28256, 14KJPN) (+ 16 more)
T=0.07390 (1396/18890, ALFA)
T=0.33902 (5682/16760, 8.3KJPN)
T=0.1309 (838/6404, 1000G_30x)
T=0.1342 (672/5008, 1000G)
T=0.0672 (301/4480, Estonian)
T=0.0688 (265/3854, ALSPAC)
T=0.0615 (228/3708, TWINSUK)
T=0.3287 (963/2930, KOREAN)
T=0.059 (59/998, GoNL)
T=0.057 (34/600, NorthernSweden)
T=0.128 (67/522, SGDP_PRJ)
T=0.134 (44/328, HapMap)
T=0.093 (20/216, Qatari)
T=0.280 (60/214, Vietnamese)
T=0.09 (5/56, Siberian)
T=0.05 (2/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MMP11 : 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	18890	T=0.07390	C=0.92610
European	Sub	14286	T=0.06965	C=0.93035
African	Sub	2946	T=0.0628	C=0.9372
African Others	Sub	114	T=0.079	C=0.921
African American	Sub	2832	T=0.0621	C=0.9379
Asian	Sub	112	T=0.232	C=0.768
East Asian	Sub	86	T=0.26	C=0.74
Other Asian	Sub	26	T=0.15	C=0.85
Latin American 1	Sub	146	T=0.062	C=0.938
Latin American 2	Sub	610	T=0.175	C=0.825
South Asian	Sub	98	T=0.12	C=0.88
Other	Sub	692	T=0.090	C=0.910

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	T=0.085050	C=0.914950
gnomAD - Genomes	Global	Study-wide	140072	T=0.075968	C=0.924032
gnomAD - Genomes	European	Sub	75898	T=0.07075	C=0.92925
gnomAD - Genomes	African	Sub	41930	T=0.06594	C=0.93406
gnomAD - Genomes	American	Sub	13640	T=0.09091	C=0.90909
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.0698	C=0.9302
gnomAD - Genomes	East Asian	Sub	3128	T=0.2698	C=0.7302
gnomAD - Genomes	Other	Sub	2152	T=0.0883	C=0.9117
14KJPN	JAPANESE	Study-wide	28256	T=0.34513	C=0.65487
Allele Frequency Aggregator	Total	Global	18890	T=0.07390	C=0.92610
Allele Frequency Aggregator	European	Sub	14286	T=0.06965	C=0.93035
Allele Frequency Aggregator	African	Sub	2946	T=0.0628	C=0.9372
Allele Frequency Aggregator	Other	Sub	692	T=0.090	C=0.910
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.175	C=0.825
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.062	C=0.938
Allele Frequency Aggregator	Asian	Sub	112	T=0.232	C=0.768
Allele Frequency Aggregator	South Asian	Sub	98	T=0.12	C=0.88
8.3KJPN	JAPANESE	Study-wide	16760	T=0.33902	C=0.66098
1000Genomes_30x	Global	Study-wide	6404	T=0.1309	C=0.8691
1000Genomes_30x	African	Sub	1786	T=0.0711	C=0.9289
1000Genomes_30x	Europe	Sub	1266	T=0.0608	C=0.9392
1000Genomes_30x	South Asian	Sub	1202	T=0.1772	C=0.8228
1000Genomes_30x	East Asian	Sub	1170	T=0.2692	C=0.7308
1000Genomes_30x	American	Sub	980	T=0.108	C=0.892
1000Genomes	Global	Study-wide	5008	T=0.1342	C=0.8658
1000Genomes	African	Sub	1322	T=0.0666	C=0.9334
1000Genomes	East Asian	Sub	1008	T=0.2698	C=0.7302
1000Genomes	Europe	Sub	1006	T=0.0567	C=0.9433
1000Genomes	South Asian	Sub	978	T=0.185	C=0.815
1000Genomes	American	Sub	694	T=0.107	C=0.893
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.0672	C=0.9328
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.0688	C=0.9312
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.0615	C=0.9385
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3287	A=0.0000, C=0.6713, G=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.059	C=0.941
Northern Sweden	ACPOP	Study-wide	600	T=0.057	C=0.943
SGDP_PRJ	Global	Study-wide	522	T=0.128	C=0.872
HapMap	Global	Study-wide	328	T=0.134	C=0.866
HapMap	African	Sub	120	T=0.067	C=0.933
HapMap	American	Sub	120	T=0.042	C=0.958
HapMap	Asian	Sub	88	T=0.35	C=0.65
Qatari	Global	Study-wide	216	T=0.093	C=0.907
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.280	C=0.720
Siberian	Global	Study-wide	56	T=0.09	C=0.91
The Danish reference pan genome	Danish	Study-wide	40	T=0.05	C=0.95

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 22	NC_000022.11:g.23774630T>A
GRCh38.p14 chr 22	NC_000022.11:g.23774630T>C
GRCh38.p14 chr 22	NC_000022.11:g.23774630T>G
GRCh37.p13 chr 22	NC_000022.10:g.24116817T>A
GRCh37.p13 chr 22	NC_000022.10:g.24116817T>C
GRCh37.p13 chr 22	NC_000022.10:g.24116817T>G
MMP11 RefSeqGene	NG_029443.1:g.6782T>A
MMP11 RefSeqGene	NG_029443.1:g.6782T>C
MMP11 RefSeqGene	NG_029443.1:g.6782T>G
GRCh38.p14 chr 22 alt locus HSCHR22_1_CTG7	NT_187633.1:g.10992T>A
GRCh38.p14 chr 22 alt locus HSCHR22_1_CTG7	NT_187633.1:g.10992T>C
GRCh38.p14 chr 22 alt locus HSCHR22_1_CTG7	NT_187633.1:g.10992T>G

Gene: MMP11, matrix metallopeptidase 11 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MMP11 transcript variant 1	NM_005940.5:c.108+1652T>A	N/A	Intron Variant
MMP11 transcript variant 2	NR_133013.2:n.	N/A	Intron 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	T=	A	C	G
GRCh38.p14 chr 22	NC_000022.11:g.23774630=	NC_000022.11:g.23774630T>A	NC_000022.11:g.23774630T>C	NC_000022.11:g.23774630T>G
GRCh37.p13 chr 22	NC_000022.10:g.24116817=	NC_000022.10:g.24116817T>A	NC_000022.10:g.24116817T>C	NC_000022.10:g.24116817T>G
MMP11 RefSeqGene	NG_029443.1:g.6782=	NG_029443.1:g.6782T>A	NG_029443.1:g.6782T>C	NG_029443.1:g.6782T>G
GRCh38.p14 chr 22 alt locus HSCHR22_1_CTG7	NT_187633.1:g.10992=	NT_187633.1:g.10992T>A	NT_187633.1:g.10992T>C	NT_187633.1:g.10992T>G
MMP11 transcript	NM_005940.3:c.108+1652=	NM_005940.3:c.108+1652T>A	NM_005940.3:c.108+1652T>C	NM_005940.3:c.108+1652T>G
MMP11 transcript variant 1	NM_005940.5:c.108+1652=	NM_005940.5:c.108+1652T>A	NM_005940.5:c.108+1652T>C	NM_005940.5:c.108+1652T>G

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#.

81 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss86316	Oct 05, 2000 (86)
2	YUSUKE	ss3223350	Sep 28, 2001 (100)
3	SC_SNP	ss7999771	Apr 21, 2003 (114)
4	SC_SNP	ss13364451	Dec 05, 2003 (119)
5	CSHL-HAPMAP	ss16918886	Feb 27, 2004 (120)
6	SSAHASNP	ss21845464	Apr 05, 2004 (121)
7	EGP_SNPS	ss35038189	May 24, 2005 (125)
8	ABI	ss44304317	Mar 14, 2006 (126)
9	HGSV	ss80180934	Dec 14, 2007 (130)
10	HGSV	ss85738422	Dec 14, 2007 (130)
11	HUMANGENOME_JCVI	ss96094708	Feb 04, 2009 (130)
12	BGI	ss103846762	Dec 01, 2009 (131)
13	1000GENOMES	ss112572152	Jan 25, 2009 (130)
14	1000GENOMES	ss114074471	Jan 25, 2009 (130)
15	ILLUMINA-UK	ss117372489	Feb 14, 2009 (130)
16	ENSEMBL	ss139895679	Dec 01, 2009 (131)
17	GMI	ss157071344	Dec 01, 2009 (131)
18	COMPLETE_GENOMICS	ss167745049	Jul 04, 2010 (132)
19	COMPLETE_GENOMICS	ss168971041	Jul 04, 2010 (132)
20	COMPLETE_GENOMICS	ss171862234	Jul 04, 2010 (132)
21	BUSHMAN	ss204059690	Jul 04, 2010 (132)
22	BCM-HGSC-SUB	ss208840240	Jul 04, 2010 (132)
23	1000GENOMES	ss228632804	Jul 14, 2010 (132)
24	1000GENOMES	ss238033257	Jul 15, 2010 (132)
25	1000GENOMES	ss244160660	Jul 15, 2010 (132)
26	BL	ss255858365	May 09, 2011 (134)
27	GMI	ss283600716	May 04, 2012 (137)
28	GMI	ss287554453	Apr 25, 2013 (138)
29	PJP	ss292742364	May 09, 2011 (134)
30	TISHKOFF	ss566579055	Apr 25, 2013 (138)
31	SSMP	ss662507320	Apr 25, 2013 (138)
32	EVA-GONL	ss995252585	Aug 21, 2014 (142)
33	JMKIDD_LAB	ss1082589927	Aug 21, 2014 (142)
34	1000GENOMES	ss1366800843	Aug 21, 2014 (142)
35	DDI	ss1429230312	Apr 01, 2015 (144)
36	EVA_GENOME_DK	ss1579715634	Apr 01, 2015 (144)
37	EVA_UK10K_ALSPAC	ss1639804429	Apr 01, 2015 (144)
38	EVA_UK10K_TWINSUK	ss1682798462	Apr 01, 2015 (144)
39	EVA_DECODE	ss1699320904	Apr 01, 2015 (144)
40	HAMMER_LAB	ss1809747315	Sep 08, 2015 (146)
41	WEILL_CORNELL_DGM	ss1938818914	Feb 12, 2016 (147)
42	GENOMED	ss1969253296	Jul 19, 2016 (147)
43	JJLAB	ss2030181848	Sep 14, 2016 (149)
44	USC_VALOUEV	ss2158793993	Dec 20, 2016 (150)
45	HUMAN_LONGEVITY	ss2246618866	Dec 20, 2016 (150)
46	SYSTEMSBIOZJU	ss2629589430	Nov 08, 2017 (151)
47	GRF	ss2704542200	Nov 08, 2017 (151)
48	GNOMAD	ss2973351097	Nov 08, 2017 (151)
49	SWEGEN	ss3019149733	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3028928273	Nov 08, 2017 (151)
51	CSHL	ss3352793456	Nov 08, 2017 (151)
52	URBANLAB	ss3651159411	Oct 12, 2018 (152)
53	EGCUT_WGS	ss3685654973	Jul 13, 2019 (153)
54	EVA_DECODE	ss3708011203	Jul 13, 2019 (153)
55	ACPOP	ss3743850042	Jul 13, 2019 (153)
56	EVA	ss3759267210	Jul 13, 2019 (153)
57	PACBIO	ss3788802364	Jul 13, 2019 (153)
58	PACBIO	ss3793672343	Jul 13, 2019 (153)
59	PACBIO	ss3798558727	Jul 13, 2019 (153)
60	KHV_HUMAN_GENOMES	ss3822434544	Jul 13, 2019 (153)
61	EVA	ss3835942584	Apr 27, 2020 (154)
62	EVA	ss3841599772	Apr 27, 2020 (154)
63	EVA	ss3847114135	Apr 27, 2020 (154)
64	SGDP_PRJ	ss3890347117	Apr 27, 2020 (154)
65	KRGDB	ss3940737880	Apr 27, 2020 (154)
66	VINODS	ss4034756314	Apr 26, 2021 (155)
67	TOPMED	ss5106035142	Apr 26, 2021 (155)
68	TOMMO_GENOMICS	ss5232198279	Apr 26, 2021 (155)
69	1000G_HIGH_COVERAGE	ss5310773867	Oct 16, 2022 (156)
70	EVA	ss5440718278	Oct 16, 2022 (156)
71	HUGCELL_USP	ss5502652146	Oct 16, 2022 (156)
72	EVA	ss5512353412	Oct 16, 2022 (156)
73	1000G_HIGH_COVERAGE	ss5618181364	Oct 16, 2022 (156)
74	SANFORD_IMAGENETICS	ss5664310405	Oct 16, 2022 (156)
75	TOMMO_GENOMICS	ss5793184748	Oct 16, 2022 (156)
76	YY_MCH	ss5818628113	Oct 16, 2022 (156)
77	EVA	ss5821943031	Oct 16, 2022 (156)
78	EVA	ss5853358646	Oct 16, 2022 (156)
79	EVA	ss5881456846	Oct 16, 2022 (156)
80	EVA	ss5959163211	Oct 16, 2022 (156)
81	EVA	ss5981127587	Oct 16, 2022 (156)
82	1000Genomes	NC_000022.10 - 24116817	Oct 12, 2018 (152)
83	1000Genomes_30x	NC_000022.11 - 23774630	Oct 16, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 24116817	Oct 12, 2018 (152)
85	Genetic variation in the Estonian population	NC_000022.10 - 24116817	Oct 12, 2018 (152)
86	The Danish reference pan genome	NC_000022.10 - 24116817	Apr 27, 2020 (154)
87	gnomAD - Genomes	NC_000022.11 - 23774630	Apr 26, 2021 (155)
88	Genome of the Netherlands Release 5	NC_000022.10 - 24116817	Apr 27, 2020 (154)
89	HapMap	NC_000022.11 - 23774630	Apr 27, 2020 (154)
90	KOREAN population from KRGDB	NC_000022.10 - 24116817	Apr 27, 2020 (154)
91	Northern Sweden	NC_000022.10 - 24116817	Jul 13, 2019 (153)
92	Qatari	NC_000022.10 - 24116817	Apr 27, 2020 (154)
93	SGDP_PRJ	NC_000022.10 - 24116817	Apr 27, 2020 (154)
94	Siberian	NC_000022.10 - 24116817	Apr 27, 2020 (154)
95	8.3KJPN	NC_000022.10 - 24116817	Apr 26, 2021 (155)
96	14KJPN	NC_000022.11 - 23774630	Oct 16, 2022 (156)
97	TopMed	NC_000022.11 - 23774630	Apr 26, 2021 (155)
98	UK 10K study - Twins	NC_000022.10 - 24116817	Oct 12, 2018 (152)
99	A Vietnamese Genetic Variation Database	NC_000022.10 - 24116817	Jul 13, 2019 (153)
100	ALFA	NC_000022.11 - 23774630	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)
rs57173180	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
47915274, ss3940737880	NC_000022.10:24116816:T:A	NC_000022.11:23774629:T:A	(self)
ss80180934, ss85738422	NC_000022.8:22441370:T:C	NC_000022.11:23774629:T:C	(self)
ss112572152, ss114074471, ss117372489, ss167745049, ss168971041, ss171862234, ss204059690, ss208840240, ss255858365, ss283600716, ss287554453, ss292742364, ss1699320904	NC_000022.9:22446816:T:C	NC_000022.11:23774629:T:C	(self)
80339318, 44438123, 31393221, 5880573, 19801127, 47915274, 17134907, 20860836, 42364097, 11310347, 90167586, 44438123, 9805940, ss228632804, ss238033257, ss244160660, ss566579055, ss662507320, ss995252585, ss1082589927, ss1366800843, ss1429230312, ss1579715634, ss1639804429, ss1682798462, ss1809747315, ss1938818914, ss1969253296, ss2030181848, ss2158793993, ss2629589430, ss2704542200, ss2973351097, ss3019149733, ss3352793456, ss3685654973, ss3743850042, ss3759267210, ss3788802364, ss3793672343, ss3798558727, ss3835942584, ss3841599772, ss3890347117, ss3940737880, ss5232198279, ss5440718278, ss5512353412, ss5664310405, ss5821943031, ss5959163211, ss5981127587	NC_000022.10:24116816:T:C	NC_000022.11:23774629:T:C	(self)
105707299, 567350296, 2233427, 127021852, 381144089, 13830999728, ss2246618866, ss3028928273, ss3651159411, ss3708011203, ss3822434544, ss3847114135, ss5106035142, ss5310773867, ss5502652146, ss5618181364, ss5793184748, ss5818628113, ss5853358646, ss5881456846	NC_000022.11:23774629:T:C	NC_000022.11:23774629:T:C	(self)
ss13364451, ss16918886, ss21845464	NT_011520.9:3507385:T:C	NC_000022.11:23774629:T:C	(self)
ss86316, ss3223350, ss7999771, ss35038189, ss44304317, ss96094708, ss103846762, ss139895679, ss157071344	NT_011520.12:3507385:T:C	NC_000022.11:23774629:T:C	(self)
ss4034756314	NT_187633.1:10991:T:C	NC_000022.11:23774629:T:C	(self)
47915274, ss3940737880	NC_000022.10:24116816:T:G	NC_000022.11:23774629:T:G	(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 rs738790

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs738790