Name: rs2472
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.

rs2472

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:94422138 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.041940 (11101/264690, TOPMED)
C=0.044451 (6225/140042, GnomAD)
C=0.05351 (1799/33622, ALFA) (+ 15 more)
C=0.0228 (146/6404, 1000G_30x)
C=0.0206 (103/5008, 1000G)
C=0.0500 (224/4480, Estonian)
C=0.0688 (265/3854, ALSPAC)
C=0.0596 (221/3708, TWINSUK)
C=0.0194 (22/1136, Daghestan)
C=0.079 (79/998, GoNL)
C=0.072 (43/600, NorthernSweden)
C=0.052 (17/330, HapMap)
C=0.005 (1/216, Qatari)
C=0.10 (4/40, GENOME_DK)
T=0.5 (3/6, SGDP_PRJ)
C=0.5 (3/6, SGDP_PRJ)
T=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)

Clinical Significance: Reported in ClinVar
Gene : Consequence: COL1A2 : Intron Variant
Publications: 1 citation
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	33622	T=0.94649	C=0.05351	0.896318	0.003331	0.100351	1
European	Sub	24798	T=0.93572	C=0.06428	0.875474	0.004033	0.120494	0
African	Sub	5798	T=0.9864	C=0.0136	0.973094	0.000345	0.026561	0
African Others	Sub	208	T=1.000	C=0.000	1.0	0.0	0.0	N/A
African American	Sub	5590	T=0.9859	C=0.0141	0.972093	0.000358	0.027549	0
Asian	Sub	130	T=1.000	C=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	102	T=1.000	C=0.000	1.0	0.0	0.0	N/A
Other Asian	Sub	28	T=1.00	C=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	166	T=0.952	C=0.048	0.903614	0.0	0.096386	0
Latin American 2	Sub	700	T=0.949	C=0.051	0.9	0.002857	0.097143	0
South Asian	Sub	116	T=1.000	C=0.000	1.0	0.0	0.0	N/A
Other	Sub	1914	T=0.9572	C=0.0428	0.918495	0.00418	0.077325	2

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	T=0.958060	C=0.041940
gnomAD - Genomes	Global	Study-wide	140042	T=0.955549	C=0.044451
gnomAD - Genomes	European	Sub	75826	T=0.93482	C=0.06518
gnomAD - Genomes	African	Sub	41982	T=0.98592	C=0.01408
gnomAD - Genomes	American	Sub	13632	T=0.96325	C=0.03675
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.9669	C=0.0331
gnomAD - Genomes	East Asian	Sub	3134	T=0.9997	C=0.0003
gnomAD - Genomes	Other	Sub	2146	T=0.9627	C=0.0373
Allele Frequency Aggregator	Total	Global	33622	T=0.94649	C=0.05351
Allele Frequency Aggregator	European	Sub	24798	T=0.93572	C=0.06428
Allele Frequency Aggregator	African	Sub	5798	T=0.9864	C=0.0136
Allele Frequency Aggregator	Other	Sub	1914	T=0.9572	C=0.0428
Allele Frequency Aggregator	Latin American 2	Sub	700	T=0.949	C=0.051
Allele Frequency Aggregator	Latin American 1	Sub	166	T=0.952	C=0.048
Allele Frequency Aggregator	Asian	Sub	130	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	116	T=1.000	C=0.000
1000Genomes_30x	Global	Study-wide	6404	T=0.9772	C=0.0228
1000Genomes_30x	African	Sub	1786	T=0.9961	C=0.0039
1000Genomes_30x	Europe	Sub	1266	T=0.9258	C=0.0742
1000Genomes_30x	South Asian	Sub	1202	T=0.9958	C=0.0042
1000Genomes_30x	East Asian	Sub	1170	T=0.9991	C=0.0009
1000Genomes_30x	American	Sub	980	T=0.960	C=0.040
1000Genomes	Global	Study-wide	5008	T=0.9794	C=0.0206
1000Genomes	African	Sub	1322	T=0.9962	C=0.0038
1000Genomes	East Asian	Sub	1008	T=0.9990	C=0.0010
1000Genomes	Europe	Sub	1006	T=0.9334	C=0.0666
1000Genomes	South Asian	Sub	978	T=0.996	C=0.004
1000Genomes	American	Sub	694	T=0.963	C=0.037
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9500	C=0.0500
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9312	C=0.0688
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9404	C=0.0596
Genome-wide autozygosity in Daghestan	Global	Study-wide	1136	T=0.9806	C=0.0194
Genome-wide autozygosity in Daghestan	Daghestan	Sub	628	T=0.979	C=0.021
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	T=0.993	C=0.007
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	T=0.984	C=0.016
Genome-wide autozygosity in Daghestan	Europe	Sub	108	T=0.944	C=0.056
Genome-wide autozygosity in Daghestan	South Asian	Sub	98	T=1.00	C=0.00
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	T=1.00	C=0.00
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.921	C=0.079
Northern Sweden	ACPOP	Study-wide	600	T=0.928	C=0.072
HapMap	Global	Study-wide	330	T=0.948	C=0.052
HapMap	African	Sub	120	T=1.000	C=0.000
HapMap	American	Sub	120	T=0.858	C=0.142
HapMap	Asian	Sub	90	T=1.00	C=0.00
Qatari	Global	Study-wide	216	T=0.995	C=0.005
The Danish reference pan genome	Danish	Study-wide	40	T=0.90	C=0.10
SGDP_PRJ	Global	Study-wide	6	T=0.5	C=0.5
Siberian	Global	Study-wide	2	T=0.5	C=0.5

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 7	NC_000007.14:g.94422138T>C
GRCh37.p13 chr 7	NC_000007.13:g.94051450T>C
COL1A2 RefSeqGene (LRG_2)	NG_007405.1:g.32578T>C

Gene: COL1A2, collagen type I alpha 2 chain (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
COL1A2 transcript	NM_000089.4:c.2403+186T>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: 663186 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000838049.1	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	T=	C
GRCh38.p14 chr 7	NC_000007.14:g.94422138=	NC_000007.14:g.94422138T>C
GRCh37.p13 chr 7	NC_000007.13:g.94051450=	NC_000007.13:g.94051450T>C
COL1A2 RefSeqGene (LRG_2)	NG_007405.1:g.32578=	NG_007405.1:g.32578T>C
COL1A2 transcript	NM_000089.3:c.2403+186=	NM_000089.3:c.2403+186T>C
COL1A2 transcript	NM_000089.4:c.2403+186=	NM_000089.4:c.2403+186T>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#.

48 SubSNP, 16 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss48238	May 08, 2000 (92)
2	LEE	ss4402745	May 29, 2002 (106)
3	PERLEGEN	ss69022538	May 16, 2007 (127)
4	1000GENOMES	ss234080289	Jul 15, 2010 (132)
5	ILLUMINA	ss244290687	Jul 04, 2010 (132)
6	ILLUMINA	ss483712981	May 04, 2012 (137)
7	ILLUMINA	ss485496971	May 04, 2012 (137)
8	ILLUMINA	ss535914035	Sep 08, 2015 (146)
9	ILLUMINA	ss779514675	Sep 08, 2015 (146)
10	ILLUMINA	ss782300022	Sep 08, 2015 (146)
11	ILLUMINA	ss834985078	Sep 08, 2015 (146)
12	EVA-GONL	ss984553831	Aug 21, 2014 (142)
13	1000GENOMES	ss1326196990	Aug 21, 2014 (142)
14	HAMMER_LAB	ss1397500650	Sep 08, 2015 (146)
15	EVA_GENOME_DK	ss1582311171	Apr 01, 2015 (144)
16	EVA_DECODE	ss1594131628	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1618726097	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1661720130	Apr 01, 2015 (144)
19	WEILL_CORNELL_DGM	ss1927813969	Feb 12, 2016 (147)
20	GENOMED	ss1970763722	Jul 19, 2016 (147)
21	JJLAB	ss2024590266	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2152811521	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2295914196	Dec 20, 2016 (150)
24	ILLUMINA	ss2634633925	Nov 08, 2017 (151)
25	GNOMAD	ss2856351260	Nov 08, 2017 (151)
26	SWEGEN	ss3001649490	Nov 08, 2017 (151)
27	BIOINF_KMB_FNS_UNIBA	ss3026087999	Nov 08, 2017 (151)
28	CSHL	ss3347736481	Nov 08, 2017 (151)
29	ILLUMINA	ss3629865699	Oct 12, 2018 (152)
30	ILLUMINA	ss3632539826	Oct 12, 2018 (152)
31	EGCUT_WGS	ss3669407030	Jul 13, 2019 (153)
32	EVA_DECODE	ss3720231036	Jul 13, 2019 (153)
33	ACPOP	ss3734872388	Jul 13, 2019 (153)
34	EVA	ss3830705556	Apr 26, 2020 (154)
35	SGDP_PRJ	ss3867909049	Apr 26, 2020 (154)
36	EVA	ss3986389283	Apr 26, 2021 (155)
37	TOPMED	ss4755310041	Apr 26, 2021 (155)
38	1000G_HIGH_COVERAGE	ss5273905216	Oct 13, 2022 (156)
39	EVA	ss5375273447	Oct 13, 2022 (156)
40	HUGCELL_USP	ss5470889533	Oct 13, 2022 (156)
41	EVA	ss5509051792	Oct 13, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5562622660	Oct 13, 2022 (156)
43	EVA	ss5624168624	Oct 13, 2022 (156)
44	SANFORD_IMAGENETICS	ss5643517232	Oct 13, 2022 (156)
45	EVA	ss5823207436	Oct 13, 2022 (156)
46	EVA	ss5848686620	Oct 13, 2022 (156)
47	EVA	ss5859944819	Oct 13, 2022 (156)
48	EVA	ss5972698058	Oct 13, 2022 (156)
49	1000Genomes	NC_000007.13 - 94051450	Oct 12, 2018 (152)
50	1000Genomes_30x	NC_000007.14 - 94422138	Oct 13, 2022 (156)
51	The Avon Longitudinal Study of Parents and Children	NC_000007.13 - 94051450	Oct 12, 2018 (152)
52	Genome-wide autozygosity in Daghestan	NC_000007.12 - 93889386	Apr 26, 2020 (154)
53	Genetic variation in the Estonian population	NC_000007.13 - 94051450	Oct 12, 2018 (152)
54	The Danish reference pan genome	NC_000007.13 - 94051450	Apr 26, 2020 (154)
55	gnomAD - Genomes	NC_000007.14 - 94422138	Apr 26, 2021 (155)
56	Genome of the Netherlands Release 5	NC_000007.13 - 94051450	Apr 26, 2020 (154)
57	HapMap	NC_000007.14 - 94422138	Apr 26, 2020 (154)
58	Northern Sweden	NC_000007.13 - 94051450	Jul 13, 2019 (153)
59	Qatari	NC_000007.13 - 94051450	Apr 26, 2020 (154)
60	SGDP_PRJ	NC_000007.13 - 94051450	Apr 26, 2020 (154)
61	Siberian	NC_000007.13 - 94051450	Apr 26, 2020 (154)
62	TopMed	NC_000007.14 - 94422138	Apr 26, 2021 (155)
63	UK 10K study - Twins	NC_000007.13 - 94051450	Oct 12, 2018 (152)
64	ALFA	NC_000007.14 - 94422138	Apr 26, 2021 (155)
65	ClinVar	RCV000838049.1	Apr 26, 2020 (154)

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)
rs42529	Jan 18, 2001 (92)
rs3180972	Jul 03, 2002 (106)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
474756, ss485496971, ss1397500650, ss1594131628	NC_000007.12:93889385:T:C	NC_000007.14:94422137:T:C	(self)
38205625, 21260019, 15145278, 8476110, 9491879, 8157253, 9855899, 19926029, 5327875, 21260019, ss234080289, ss483712981, ss535914035, ss779514675, ss782300022, ss834985078, ss984553831, ss1326196990, ss1582311171, ss1618726097, ss1661720130, ss1927813969, ss1970763722, ss2024590266, ss2152811521, ss2634633925, ss2856351260, ss3001649490, ss3347736481, ss3629865699, ss3632539826, ss3669407030, ss3734872388, ss3830705556, ss3867909049, ss3986389283, ss5375273447, ss5509051792, ss5624168624, ss5643517232, ss5823207436, ss5848686620, ss5972698058	NC_000007.13:94051449:T:C	NC_000007.14:94422137:T:C	(self)
RCV000838049.1, 50148595, 269580599, 3449164, 592687600, 9437262968, ss2295914196, ss3026087999, ss3720231036, ss4755310041, ss5273905216, ss5470889533, ss5562622660, ss5859944819	NC_000007.14:94422137:T:C	NC_000007.14:94422137:T:C	(self)
ss48238, ss4402745, ss69022538, ss244290687	NT_007933.15:32084292:T:C	NC_000007.14:94422137:T:C	(self)

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

1 citation for rs2472

PMID	Title	Author	Year	Journal
20140262	Maternal and fetal genetic associations of PTGER3 and PON1 with preterm birth.	Ryckman KK et al.	2010	PloS one

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2472