Name: rs13028444
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.

rs13028444

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:189011412 (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: A>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.239299 (63340/264690, TOPMED)
C=0.236185 (33082/140068, GnomAD)
C=0.22050 (18821/85356, ALFA) (+ 19 more)
C=0.09966 (2816/28256, 14KJPN)
C=0.10042 (1683/16760, 8.3KJPN)
C=0.2032 (1301/6404, 1000G_30x)
C=0.2047 (1025/5008, 1000G)
C=0.1719 (770/4480, Estonian)
C=0.2164 (834/3854, ALSPAC)
C=0.2149 (797/3708, TWINSUK)
C=0.0857 (251/2930, KOREAN)
C=0.2082 (433/2080, HGDP_Stanford)
C=0.2397 (453/1890, HapMap)
C=0.0906 (166/1832, Korea1K)
C=0.211 (211/998, GoNL)
C=0.170 (102/600, NorthernSweden)
C=0.407 (88/216, Qatari)
C=0.079 (17/216, Vietnamese)
A=0.417 (80/192, SGDP_PRJ)
C=0.45 (36/80, Ancient Sardinia)
C=0.12 (5/40, GENOME_DK)
A=0.4 (3/8, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: COL3A1 : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	85356	A=0.77950	C=0.22050	0.609073	0.050073	0.340855	2
European	Sub	72792	A=0.78374	C=0.21626	0.614793	0.047313	0.337894	0
African	Sub	4502	A=0.6904	C=0.3096	0.47801	0.09729	0.4247	0
African Others	Sub	170	A=0.671	C=0.329	0.423529	0.082353	0.494118	1
African American	Sub	4332	A=0.6911	C=0.3089	0.480148	0.097876	0.421976	0
Asian	Sub	230	A=0.913	C=0.087	0.826087	0.0	0.173913	1
East Asian	Sub	190	A=0.905	C=0.095	0.810526	0.0	0.189474	1
Other Asian	Sub	40	A=0.95	C=0.05	0.9	0.0	0.1	0
Latin American 1	Sub	246	A=0.691	C=0.309	0.504065	0.121951	0.373984	1
Latin American 2	Sub	1226	A=0.8687	C=0.1313	0.752039	0.014682	0.233279	0
South Asian	Sub	4952	A=0.7742	C=0.2258	0.602989	0.054523	0.342488	1
Other	Sub	1408	A=0.7798	C=0.2202	0.612216	0.052557	0.335227	0

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	A=0.760701	C=0.239299
gnomAD - Genomes	Global	Study-wide	140068	A=0.763815	C=0.236185
gnomAD - Genomes	European	Sub	75870	A=0.79135	C=0.20865
gnomAD - Genomes	African	Sub	41950	A=0.69046	C=0.30954
gnomAD - Genomes	American	Sub	13646	A=0.81262	C=0.18738
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.7058	C=0.2942
gnomAD - Genomes	East Asian	Sub	3130	A=0.9268	C=0.0732
gnomAD - Genomes	Other	Sub	2148	A=0.7658	C=0.2342
Allele Frequency Aggregator	Total	Global	85356	A=0.77950	C=0.22050
Allele Frequency Aggregator	European	Sub	72792	A=0.78374	C=0.21626
Allele Frequency Aggregator	South Asian	Sub	4952	A=0.7742	C=0.2258
Allele Frequency Aggregator	African	Sub	4502	A=0.6904	C=0.3096
Allele Frequency Aggregator	Other	Sub	1408	A=0.7798	C=0.2202
Allele Frequency Aggregator	Latin American 2	Sub	1226	A=0.8687	C=0.1313
Allele Frequency Aggregator	Latin American 1	Sub	246	A=0.691	C=0.309
Allele Frequency Aggregator	Asian	Sub	230	A=0.913	C=0.087
14KJPN	JAPANESE	Study-wide	28256	A=0.90034	C=0.09966
8.3KJPN	JAPANESE	Study-wide	16760	A=0.89958	C=0.10042
1000Genomes_30x	Global	Study-wide	6404	A=0.7968	C=0.2032
1000Genomes_30x	African	Sub	1786	A=0.6960	C=0.3040
1000Genomes_30x	Europe	Sub	1266	A=0.7678	C=0.2322
1000Genomes_30x	South Asian	Sub	1202	A=0.7879	C=0.2121
1000Genomes_30x	East Asian	Sub	1170	A=0.9325	C=0.0675
1000Genomes_30x	American	Sub	980	A=0.867	C=0.133
1000Genomes	Global	Study-wide	5008	A=0.7953	C=0.2047
1000Genomes	African	Sub	1322	A=0.6899	C=0.3101
1000Genomes	East Asian	Sub	1008	A=0.9335	C=0.0665
1000Genomes	Europe	Sub	1006	A=0.7634	C=0.2366
1000Genomes	South Asian	Sub	978	A=0.781	C=0.219
1000Genomes	American	Sub	694	A=0.862	C=0.138
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.8281	C=0.1719
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.7836	C=0.2164
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.7851	C=0.2149
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.9143	C=0.0857
HGDP-CEPH-db Supplement 1	Global	Study-wide	2080	A=0.7918	C=0.2082
HGDP-CEPH-db Supplement 1	Est_Asia	Sub	468	A=0.904	C=0.096
HGDP-CEPH-db Supplement 1	Central_South_Asia	Sub	412	A=0.757	C=0.243
HGDP-CEPH-db Supplement 1	Middle_Est	Sub	350	A=0.651	C=0.349
HGDP-CEPH-db Supplement 1	Europe	Sub	320	A=0.778	C=0.222
HGDP-CEPH-db Supplement 1	Africa	Sub	242	A=0.773	C=0.227
HGDP-CEPH-db Supplement 1	America	Sub	216	A=1.000	C=0.000
HGDP-CEPH-db Supplement 1	Oceania	Sub	72	A=0.44	C=0.56
HapMap	Global	Study-wide	1890	A=0.7603	C=0.2397
HapMap	American	Sub	770	A=0.825	C=0.175
HapMap	African	Sub	690	A=0.652	C=0.348
HapMap	Asian	Sub	254	A=0.921	C=0.079
HapMap	Europe	Sub	176	A=0.670	C=0.330
Korean Genome Project	KOREAN	Study-wide	1832	A=0.9094	C=0.0906
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.789	C=0.211
Northern Sweden	ACPOP	Study-wide	600	A=0.830	C=0.170
Qatari	Global	Study-wide	216	A=0.593	C=0.407
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.921	C=0.079
SGDP_PRJ	Global	Study-wide	192	A=0.417	C=0.583
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	80	A=0.55	C=0.45
The Danish reference pan genome	Danish	Study-wide	40	A=0.88	C=0.12
Siberian	Global	Study-wide	8	A=0.4	C=0.6

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 2	NC_000002.12:g.189011412A>C
GRCh37.p13 chr 2	NC_000002.11:g.189876138A>C
COL3A1 RefSeqGene (LRG_3)	NG_007404.1:g.42040A>C
GRCh38.p14 chr 2 fix patch HG2494_PATCH	NW_025791764.1:g.116372A>C

Gene: COL3A1, collagen type III alpha 1 chain (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
COL3A1 transcript	NM_000090.4:c.4255-216A>C	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.

Allele: C (allele ID: 1281322 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001713449.1	not provided	Benign

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	A=	C
GRCh38.p14 chr 2	NC_000002.12:g.189011412=	NC_000002.12:g.189011412A>C
GRCh37.p13 chr 2	NC_000002.11:g.189876138=	NC_000002.11:g.189876138A>C
COL3A1 RefSeqGene (LRG_3)	NG_007404.1:g.42040=	NG_007404.1:g.42040A>C
GRCh38.p14 chr 2 fix patch HG2494_PATCH	NW_025791764.1:g.116372=	NW_025791764.1:g.116372A>C
COL3A1 transcript	NM_000090.3:c.4255-216=	NM_000090.3:c.4255-216A>C
COL3A1 transcript	NM_000090.4:c.4255-216=	NM_000090.4:c.4255-216A>C

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#.

80 SubSNP, 22 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss21724748	Apr 05, 2004 (121)
2	ABI	ss44314240	Mar 15, 2006 (126)
3	ILLUMINA	ss67053196	Nov 30, 2006 (127)
4	ILLUMINA	ss67379730	Nov 30, 2006 (127)
5	ILLUMINA	ss68143493	Dec 12, 2006 (127)
6	ILLUMINA	ss70591960	May 24, 2008 (130)
7	ILLUMINA	ss71135774	May 17, 2007 (127)
8	ILLUMINA	ss75840281	Dec 06, 2007 (129)
9	HGSV	ss80680814	Dec 14, 2007 (130)
10	KRIBB_YJKIM	ss85294480	Dec 14, 2007 (130)
11	HUMANGENOME_JCVI	ss97108858	Feb 04, 2009 (130)
12	1000GENOMES	ss110465392	Jan 24, 2009 (130)
13	ILLUMINA-UK	ss118014508	Feb 14, 2009 (130)
14	ENSEMBL	ss132889503	Dec 01, 2009 (131)
15	ILLUMINA	ss153310515	Dec 01, 2009 (131)
16	ILLUMINA	ss159242585	Dec 01, 2009 (131)
17	ILLUMINA	ss172307720	Jul 04, 2010 (132)
18	BUSHMAN	ss201517324	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss205844030	Jul 04, 2010 (132)
20	1000GENOMES	ss219716394	Jul 14, 2010 (132)
21	1000GENOMES	ss231517692	Jul 14, 2010 (132)
22	1000GENOMES	ss238994936	Jul 15, 2010 (132)
23	GMI	ss276833671	May 04, 2012 (137)
24	PJP	ss292447116	May 09, 2011 (134)
25	TISHKOFF	ss556108438	Apr 25, 2013 (138)
26	SSMP	ss649771411	Apr 25, 2013 (138)
27	ILLUMINA	ss832754893	Aug 21, 2014 (142)
28	ILLUMINA	ss833345723	Aug 21, 2014 (142)
29	EVA-GONL	ss977770840	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1069799051	Aug 21, 2014 (142)
31	1000GENOMES	ss1300902445	Aug 21, 2014 (142)
32	DDI	ss1428856998	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1579249626	Apr 01, 2015 (144)
34	EVA_DECODE	ss1587215900	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1605401790	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1648395823	Apr 01, 2015 (144)
37	EVA_SVP	ss1712517906	Apr 01, 2015 (144)
38	WEILL_CORNELL_DGM	ss1921018776	Feb 12, 2016 (147)
39	JJLAB	ss2021050364	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2149115038	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2237577858	Dec 20, 2016 (150)
42	GRF	ss2703757828	Nov 08, 2017 (151)
43	ILLUMINA	ss2710920945	Nov 08, 2017 (151)
44	GNOMAD	ss2784182315	Nov 08, 2017 (151)
45	SWEGEN	ss2991059726	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3024286137	Nov 08, 2017 (151)
47	CSHL	ss3344662036	Nov 08, 2017 (151)
48	ILLUMINA	ss3625772432	Oct 11, 2018 (152)
49	ILLUMINA	ss3638308508	Oct 11, 2018 (152)
50	ILLUMINA	ss3639158091	Oct 11, 2018 (152)
51	ILLUMINA	ss3639883280	Oct 11, 2018 (152)
52	ILLUMINA	ss3643273962	Oct 11, 2018 (152)
53	ILLUMINA	ss3643931301	Oct 11, 2018 (152)
54	URBANLAB	ss3647233829	Oct 11, 2018 (152)
55	EGCUT_WGS	ss3658941408	Jul 13, 2019 (153)
56	EVA_DECODE	ss3705658815	Jul 13, 2019 (153)
57	ACPOP	ss3729214109	Jul 13, 2019 (153)
58	EVA	ss3757865239	Jul 13, 2019 (153)
59	KHV_HUMAN_GENOMES	ss3802223726	Jul 13, 2019 (153)
60	EVA	ss3827414748	Apr 25, 2020 (154)
61	HGDP	ss3847645370	Apr 25, 2020 (154)
62	SGDP_PRJ	ss3854218746	Apr 25, 2020 (154)
63	KRGDB	ss3899883433	Apr 25, 2020 (154)
64	KOGIC	ss3949724390	Apr 25, 2020 (154)
65	EVA	ss3984943506	Apr 26, 2021 (155)
66	EVA	ss4017040215	Apr 26, 2021 (155)
67	TOPMED	ss4537978150	Apr 26, 2021 (155)
68	TOMMO_GENOMICS	ss5155653580	Apr 26, 2021 (155)
69	1000G_HIGH_COVERAGE	ss5251382070	Oct 17, 2022 (156)
70	EVA	ss5334850643	Oct 17, 2022 (156)
71	HUGCELL_USP	ss5451062574	Oct 17, 2022 (156)
72	1000G_HIGH_COVERAGE	ss5528389427	Oct 17, 2022 (156)
73	SANFORD_IMAGENETICS	ss5630588856	Oct 17, 2022 (156)
74	TOMMO_GENOMICS	ss5686289307	Oct 17, 2022 (156)
75	YY_MCH	ss5803069336	Oct 17, 2022 (156)
76	EVA	ss5821342046	Oct 17, 2022 (156)
77	EVA	ss5852881340	Oct 17, 2022 (156)
78	EVA	ss5933958828	Oct 17, 2022 (156)
79	EVA	ss5956829167	Oct 17, 2022 (156)
80	EVA	ss5980101851	Oct 17, 2022 (156)
81	1000Genomes	NC_000002.11 - 189876138	Oct 11, 2018 (152)
82	1000Genomes_30x	NC_000002.12 - 189011412	Oct 17, 2022 (156)
83	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 189876138	Oct 11, 2018 (152)
84	Genetic variation in the Estonian population	NC_000002.11 - 189876138	Oct 11, 2018 (152)
85	The Danish reference pan genome	NC_000002.11 - 189876138	Apr 25, 2020 (154)
86	gnomAD - Genomes	NC_000002.12 - 189011412	Apr 26, 2021 (155)
87	Genome of the Netherlands Release 5	NC_000002.11 - 189876138	Apr 25, 2020 (154)
88	HGDP-CEPH-db Supplement 1	NC_000002.10 - 189584383	Apr 25, 2020 (154)
89	HapMap	NC_000002.12 - 189011412	Apr 25, 2020 (154)
90	KOREAN population from KRGDB	NC_000002.11 - 189876138	Apr 25, 2020 (154)
91	Korean Genome Project	NC_000002.12 - 189011412	Apr 25, 2020 (154)
92	Northern Sweden	NC_000002.11 - 189876138	Jul 13, 2019 (153)
93	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000002.11 - 189876138	Apr 26, 2021 (155)
94	Qatari	NC_000002.11 - 189876138	Apr 25, 2020 (154)
95	SGDP_PRJ	NC_000002.11 - 189876138	Apr 25, 2020 (154)
96	Siberian	NC_000002.11 - 189876138	Apr 25, 2020 (154)
97	8.3KJPN	NC_000002.11 - 189876138	Apr 26, 2021 (155)
98	14KJPN	NC_000002.12 - 189011412	Oct 17, 2022 (156)
99	TopMed	NC_000002.12 - 189011412	Apr 26, 2021 (155)
100	UK 10K study - Twins	NC_000002.11 - 189876138	Oct 11, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000002.11 - 189876138	Jul 13, 2019 (153)
102	ALFA	NC_000002.12 - 189011412	Apr 26, 2021 (155)
103	ClinVar	RCV001713449.1	Oct 17, 2022 (156)

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)
rs57793059	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss80680814, ss3639158091, ss3639883280, ss3643931301	NC_000002.9:189701643:A:C	NC_000002.12:189011411:A:C	(self)
323262, ss110465392, ss118014508, ss201517324, ss205844030, ss276833671, ss292447116, ss1587215900, ss1712517906, ss3643273962, ss3847645370	NC_000002.10:189584382:A:C	NC_000002.12:189011411:A:C	(self)
11978779, 6618938, 4679656, 5414565, 2908067, 7060827, 2498974, 169433, 3060706, 6235726, 1631392, 13622887, 6618938, 1443197, ss219716394, ss231517692, ss238994936, ss556108438, ss649771411, ss832754893, ss833345723, ss977770840, ss1069799051, ss1300902445, ss1428856998, ss1579249626, ss1605401790, ss1648395823, ss1921018776, ss2021050364, ss2149115038, ss2703757828, ss2710920945, ss2784182315, ss2991059726, ss3344662036, ss3625772432, ss3638308508, ss3658941408, ss3729214109, ss3757865239, ss3827414748, ss3854218746, ss3899883433, ss3984943506, ss4017040215, ss5155653580, ss5334850643, ss5630588856, ss5821342046, ss5956829167, ss5980101851	NC_000002.11:189876137:A:C	NC_000002.12:189011411:A:C	(self)
RCV001713449.1, 15915362, 85379231, 1974218, 6102391, 20126411, 341801029, 12493605380, ss2237577858, ss3024286137, ss3647233829, ss3705658815, ss3802223726, ss3949724390, ss4537978150, ss5251382070, ss5451062574, ss5528389427, ss5686289307, ss5803069336, ss5852881340, ss5933958828	NC_000002.12:189011411:A:C	NC_000002.12:189011411:A:C	(self)
ss21724748	NT_005403.14:40085553:A:C	NC_000002.12:189011411:A:C	(self)
ss44314240, ss67053196, ss67379730, ss68143493, ss70591960, ss71135774, ss75840281, ss85294480, ss97108858, ss132889503, ss153310515, ss159242585, ss172307720	NT_005403.17:40085555:A:C	NC_000002.12:189011411:A:C	(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 rs13028444

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

rs13028444