Name: rs2069946
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.

rs2069946

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:35174232 (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=0.047837 (12662/264690, TOPMED)
C=0.047445 (6647/140100, GnomAD)
C=0.04118 (3241/78694, PAGE_STUDY) (+ 14 more)
C=0.00007 (2/28258, 14KJPN)
C=0.04750 (1102/23200, ALFA)
C=0.00006 (1/16760, 8.3KJPN)
C=0.0336 (215/6404, 1000G_30x)
C=0.0319 (160/5008, 1000G)
C=0.0493 (221/4480, Estonian)
C=0.0410 (158/3854, ALSPAC)
C=0.0510 (189/3708, TWINSUK)
C=0.047 (47/998, GoNL)
C=0.052 (31/600, NorthernSweden)
C=0.111 (24/216, Qatari)
C=0.05 (2/40, GENOME_DK)
T=0.50 (16/32, SGDP_PRJ)
C=0.50 (16/32, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MMP24-AS1-EDEM2 : Intron Variant
PROCR : 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	23200	T=0.95250	C=0.04750
European	Sub	16532	T=0.95227	C=0.04773
African	Sub	4516	T=0.9495	C=0.0505
African Others	Sub	144	T=0.951	C=0.049
African American	Sub	4372	T=0.9495	C=0.0505
Asian	Sub	150	T=0.993	C=0.007
East Asian	Sub	122	T=1.000	C=0.000
Other Asian	Sub	28	T=0.96	C=0.04
Latin American 1	Sub	154	T=0.929	C=0.071
Latin American 2	Sub	616	T=0.974	C=0.026
South Asian	Sub	104	T=0.971	C=0.029
Other	Sub	1128	T=0.9521	C=0.0479

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=0.952163	C=0.047837
gnomAD - Genomes	Global	Study-wide	140100	T=0.952555	C=0.047445
gnomAD - Genomes	European	Sub	75884	T=0.95439	C=0.04561
gnomAD - Genomes	African	Sub	41970	T=0.94687	C=0.05313
gnomAD - Genomes	American	Sub	13640	T=0.95762	C=0.04238
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.9196	C=0.0804
gnomAD - Genomes	East Asian	Sub	3130	T=1.0000	C=0.0000
gnomAD - Genomes	Other	Sub	2154	T=0.9485	C=0.0515
The PAGE Study	Global	Study-wide	78694	T=0.95882	C=0.04118
The PAGE Study	AfricanAmerican	Sub	32512	T=0.94528	C=0.05472
The PAGE Study	Mexican	Sub	10810	T=0.96901	C=0.03099
The PAGE Study	Asian	Sub	8318	T=0.9999	C=0.0001
The PAGE Study	PuertoRican	Sub	7914	T=0.9541	C=0.0459
The PAGE Study	NativeHawaiian	Sub	4534	T=0.9850	C=0.0150
The PAGE Study	Cuban	Sub	4230	T=0.9404	C=0.0596
The PAGE Study	Dominican	Sub	3828	T=0.9438	C=0.0562
The PAGE Study	CentralAmerican	Sub	2450	T=0.9620	C=0.0380
The PAGE Study	SouthAmerican	Sub	1982	T=0.9667	C=0.0333
The PAGE Study	NativeAmerican	Sub	1260	T=0.9643	C=0.0357
The PAGE Study	SouthAsian	Sub	856	T=0.972	C=0.028
14KJPN	JAPANESE	Study-wide	28258	T=0.99993	C=0.00007
Allele Frequency Aggregator	Total	Global	23200	T=0.95250	C=0.04750
Allele Frequency Aggregator	European	Sub	16532	T=0.95227	C=0.04773
Allele Frequency Aggregator	African	Sub	4516	T=0.9495	C=0.0505
Allele Frequency Aggregator	Other	Sub	1128	T=0.9521	C=0.0479
Allele Frequency Aggregator	Latin American 2	Sub	616	T=0.974	C=0.026
Allele Frequency Aggregator	Latin American 1	Sub	154	T=0.929	C=0.071
Allele Frequency Aggregator	Asian	Sub	150	T=0.993	C=0.007
Allele Frequency Aggregator	South Asian	Sub	104	T=0.971	C=0.029
8.3KJPN	JAPANESE	Study-wide	16760	T=0.99994	C=0.00006
1000Genomes_30x	Global	Study-wide	6404	T=0.9664	C=0.0336
1000Genomes_30x	African	Sub	1786	T=0.9462	C=0.0538
1000Genomes_30x	Europe	Sub	1266	T=0.9566	C=0.0434
1000Genomes_30x	South Asian	Sub	1202	T=0.9825	C=0.0175
1000Genomes_30x	East Asian	Sub	1170	T=0.9983	C=0.0017
1000Genomes_30x	American	Sub	980	T=0.958	C=0.042
1000Genomes	Global	Study-wide	5008	T=0.9681	C=0.0319
1000Genomes	African	Sub	1322	T=0.9493	C=0.0507
1000Genomes	East Asian	Sub	1008	T=0.9980	C=0.0020
1000Genomes	Europe	Sub	1006	T=0.9592	C=0.0408
1000Genomes	South Asian	Sub	978	T=0.980	C=0.020
1000Genomes	American	Sub	694	T=0.957	C=0.043
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9507	C=0.0493
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9590	C=0.0410
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9490	C=0.0510
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.953	C=0.047
Northern Sweden	ACPOP	Study-wide	600	T=0.948	C=0.052
Qatari	Global	Study-wide	216	T=0.889	C=0.111
The Danish reference pan genome	Danish	Study-wide	40	T=0.95	C=0.05
SGDP_PRJ	Global	Study-wide	32	T=0.50	C=0.50

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 20	NC_000020.11:g.35174232T>C
GRCh37.p13 chr 20	NC_000020.10:g.33762035T>C
PROCR RefSeqGene (LRG_638)	NG_032899.2:g.7262T>C

Gene: MMP24-AS1-EDEM2, MMP24-AS1-EDEM2 readthrough (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MMP24-AS1-EDEM2 transcript	NM_001355008.2:c.-101-836… NM_001355008.2:c.-101-8361A>G	N/A	Intron Variant

Gene: PROCR, protein C receptor (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PROCR transcript	NM_006404.5:c.71-470T>C	N/A	Intron Variant
PROCR transcript variant X2	XM_011528496.2:c.182-470T… XM_011528496.2:c.182-470T>C	N/A	Intron Variant
PROCR transcript variant X1	XM_047439830.1:c.182-470T… XM_047439830.1:c.182-470T>C	N/A	Intron Variant
PROCR transcript variant X3	XM_047439831.1:c.71-470T>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.

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=	C
GRCh38.p14 chr 20	NC_000020.11:g.35174232=	NC_000020.11:g.35174232T>C
GRCh37.p13 chr 20	NC_000020.10:g.33762035=	NC_000020.10:g.33762035T>C
PROCR RefSeqGene (LRG_638)	NG_032899.2:g.7262=	NG_032899.2:g.7262T>C
MMP24-AS1-EDEM2 transcript	NM_001355008.2:c.-101-8361=	NM_001355008.2:c.-101-8361A>G
PROCR transcript	NM_006404.4:c.71-470=	NM_006404.4:c.71-470T>C
PROCR transcript	NM_006404.5:c.71-470=	NM_006404.5:c.71-470T>C
PROCR transcript variant X1	XM_005260251.1:c.71-470=	XM_005260251.1:c.71-470T>C
PROCR transcript variant X2	XM_011528496.2:c.182-470=	XM_011528496.2:c.182-470T>C
PROCR transcript variant X1	XM_047439830.1:c.182-470=	XM_047439830.1:c.182-470T>C
PROCR transcript variant X3	XM_047439831.1:c.71-470=	XM_047439831.1:c.71-470T>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#.

59 SubSNP, 16 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PGA-UW-FHCRC	ss2982086	Jun 15, 2001 (96)
2	1000GENOMES	ss113291343	Jan 25, 2009 (130)
3	ILLUMINA-UK	ss117534085	Feb 14, 2009 (130)
4	COMPLETE_GENOMICS	ss169515540	Jul 04, 2010 (132)
5	ILLUMINA	ss173094499	Jul 04, 2010 (132)
6	BUSHMAN	ss203878601	Jul 04, 2010 (132)
7	1000GENOMES	ss228335912	Jul 14, 2010 (132)
8	1000GENOMES	ss237820552	Jul 15, 2010 (132)
9	GMI	ss287453306	Apr 25, 2013 (138)
10	ILLUMINA	ss537033697	Sep 08, 2015 (146)
11	TISHKOFF	ss566227357	Apr 25, 2013 (138)
12	SSMP	ss662110012	Apr 25, 2013 (138)
13	EVA-GONL	ss994689643	Aug 21, 2014 (142)
14	JMKIDD_LAB	ss1082181517	Aug 21, 2014 (142)
15	1000GENOMES	ss1364648777	Aug 21, 2014 (142)
16	EVA_GENOME_DK	ss1579495122	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1638714428	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1681708461	Apr 01, 2015 (144)
19	EVA_DECODE	ss1698748195	Apr 01, 2015 (144)
20	WEILL_CORNELL_DGM	ss1938202772	Feb 12, 2016 (147)
21	ILLUMINA	ss1959912181	Feb 12, 2016 (147)
22	JJLAB	ss2029883340	Sep 14, 2016 (149)
23	HUMAN_LONGEVITY	ss2242496959	Dec 20, 2016 (150)
24	GNOMAD	ss2967074385	Nov 08, 2017 (151)
25	SWEGEN	ss3018136480	Nov 08, 2017 (151)
26	ILLUMINA	ss3022115837	Nov 08, 2017 (151)
27	CSHL	ss3352498963	Nov 08, 2017 (151)
28	ILLUMINA	ss3628383585	Oct 12, 2018 (152)
29	ILLUMINA	ss3638343684	Oct 12, 2018 (152)
30	BIOINF_KMB_FNS_UNIBA	ss3645643953	Oct 12, 2018 (152)
31	ILLUMINA	ss3652570888	Oct 12, 2018 (152)
32	EGCUT_WGS	ss3684816100	Jul 13, 2019 (153)
33	EVA_DECODE	ss3706886396	Jul 13, 2019 (153)
34	ILLUMINA	ss3725912296	Jul 13, 2019 (153)
35	ACPOP	ss3743369024	Jul 13, 2019 (153)
36	EVA	ss3758604056	Jul 13, 2019 (153)
37	PAGE_CC	ss3772045605	Jul 13, 2019 (153)
38	PACBIO	ss3788640606	Jul 13, 2019 (153)
39	PACBIO	ss3793533962	Jul 13, 2019 (153)
40	PACBIO	ss3798420857	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3821771914	Jul 13, 2019 (153)
42	EVA	ss3835658460	Apr 27, 2020 (154)
43	SGDP_PRJ	ss3889040419	Apr 27, 2020 (154)
44	EVA	ss4017846022	Apr 27, 2021 (155)
45	TOPMED	ss5087538129	Apr 27, 2021 (155)
46	TOMMO_GENOMICS	ss5229506692	Apr 27, 2021 (155)
47	EVA	ss5237604780	Apr 27, 2021 (155)
48	1000G_HIGH_COVERAGE	ss5308691973	Oct 16, 2022 (156)
49	EVA	ss5437205505	Oct 16, 2022 (156)
50	HUGCELL_USP	ss5500979736	Oct 16, 2022 (156)
51	EVA	ss5512207915	Oct 16, 2022 (156)
52	1000G_HIGH_COVERAGE	ss5615100156	Oct 16, 2022 (156)
53	SANFORD_IMAGENETICS	ss5624484582	Oct 16, 2022 (156)
54	SANFORD_IMAGENETICS	ss5663156427	Oct 16, 2022 (156)
55	TOMMO_GENOMICS	ss5789262795	Oct 16, 2022 (156)
56	EVA	ss5845653476	Oct 16, 2022 (156)
57	EVA	ss5923302203	Oct 16, 2022 (156)
58	EVA	ss5958066651	Oct 16, 2022 (156)
59	EVA	ss5979614947	Oct 16, 2022 (156)
60	1000Genomes	NC_000020.10 - 33762035	Oct 12, 2018 (152)
61	1000Genomes_30x	NC_000020.11 - 35174232	Oct 16, 2022 (156)
62	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 33762035	Oct 12, 2018 (152)
63	Genetic variation in the Estonian population	NC_000020.10 - 33762035	Oct 12, 2018 (152)
64	The Danish reference pan genome	NC_000020.10 - 33762035	Apr 27, 2020 (154)
65	gnomAD - Genomes	NC_000020.11 - 35174232	Apr 27, 2021 (155)
66	Genome of the Netherlands Release 5	NC_000020.10 - 33762035	Apr 27, 2020 (154)
67	Northern Sweden	NC_000020.10 - 33762035	Jul 13, 2019 (153)
68	The PAGE Study	NC_000020.11 - 35174232	Jul 13, 2019 (153)
69	Qatari	NC_000020.10 - 33762035	Apr 27, 2020 (154)
70	SGDP_PRJ	NC_000020.10 - 33762035	Apr 27, 2020 (154)
71	8.3KJPN	NC_000020.10 - 33762035	Apr 27, 2021 (155)
72	14KJPN	NC_000020.11 - 35174232	Oct 16, 2022 (156)
73	TopMed	NC_000020.11 - 35174232	Apr 27, 2021 (155)
74	UK 10K study - Twins	NC_000020.10 - 33762035	Oct 12, 2018 (152)
75	ALFA	NC_000020.11 - 35174232	Apr 27, 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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss113291343, ss117534085, ss169515540, ss203878601, ss287453306, ss1698748195	NC_000020.9:33225695:T:C	NC_000020.11:35174231:T:C	(self)
78107927, 43235794, 30554348, 5660061, 19263729, 16653889, 20244694, 41057399, 87475999, 43235794, ss228335912, ss237820552, ss537033697, ss566227357, ss662110012, ss994689643, ss1082181517, ss1364648777, ss1579495122, ss1638714428, ss1681708461, ss1938202772, ss1959912181, ss2029883340, ss2967074385, ss3018136480, ss3022115837, ss3352498963, ss3628383585, ss3638343684, ss3652570888, ss3684816100, ss3743369024, ss3758604056, ss3788640606, ss3793533962, ss3798420857, ss3835658460, ss3889040419, ss4017846022, ss5229506692, ss5237604780, ss5437205505, ss5512207915, ss5624484582, ss5663156427, ss5845653476, ss5958066651, ss5979614947	NC_000020.10:33762034:T:C	NC_000020.11:35174231:T:C	(self)
102626091, 550969651, 1267074, 123099899, 362647074, 2280157915, ss2242496959, ss3645643953, ss3706886396, ss3725912296, ss3772045605, ss3821771914, ss5087538129, ss5308691973, ss5500979736, ss5615100156, ss5789262795, ss5923302203	NC_000020.11:35174231:T:C	NC_000020.11:35174231:T:C	(self)
ss2982086, ss173094499	NT_011362.10:3958126:T:C	NC_000020.11:35174231:T: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 rs2069946

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

rs2069946