Name: rs2028086
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.

rs2028086

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr8:96591950 (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: G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.168559 (44616/264690, TOPMED)
C=0.180448 (25271/140046, GnomAD)
C=0.26021 (7353/28258, 14KJPN) (+ 17 more)
C=0.21016 (3970/18890, ALFA)
C=0.25907 (4342/16760, 8.3KJPN)
C=0.2106 (1349/6404, 1000G_30x)
C=0.2208 (1106/5008, 1000G)
C=0.2821 (1264/4480, Estonian)
C=0.2094 (807/3854, ALSPAC)
C=0.2268 (841/3708, TWINSUK)
C=0.2618 (767/2930, KOREAN)
C=0.2000 (378/1890, HapMap)
C=0.2500 (458/1832, Korea1K)
C=0.241 (241/998, GoNL)
C=0.207 (124/600, NorthernSweden)
G=0.427 (100/234, SGDP_PRJ)
C=0.199 (43/216, Qatari)
C=0.368 (78/212, Vietnamese)
C=0.33 (13/40, GENOME_DK)
G=0.42 (11/26, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SDC2 : 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18890	G=0.78984	C=0.21016
European	Sub	14286	G=0.75570	C=0.24430
African	Sub	2946	G=0.9413	C=0.0587
African Others	Sub	114	G=0.965	C=0.035
African American	Sub	2832	G=0.9403	C=0.0597
Asian	Sub	112	G=0.750	C=0.250
East Asian	Sub	86	G=0.79	C=0.21
Other Asian	Sub	26	G=0.62	C=0.38
Latin American 1	Sub	146	G=0.829	C=0.171
Latin American 2	Sub	610	G=0.839	C=0.161
South Asian	Sub	98	G=0.58	C=0.42
Other	Sub	692	G=0.834	C=0.166

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	G=0.831441	C=0.168559
gnomAD - Genomes	Global	Study-wide	140046	G=0.819552	C=0.180448
gnomAD - Genomes	European	Sub	75832	G=0.76179	C=0.23821
gnomAD - Genomes	African	Sub	41992	G=0.93558	C=0.06442
gnomAD - Genomes	American	Sub	13628	G=0.83446	C=0.16554
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=0.7807	C=0.2193
gnomAD - Genomes	East Asian	Sub	3122	G=0.6438	C=0.3562
gnomAD - Genomes	Other	Sub	2152	G=0.8113	C=0.1887
14KJPN	JAPANESE	Study-wide	28258	G=0.73979	C=0.26021
Allele Frequency Aggregator	Total	Global	18890	G=0.78984	C=0.21016
Allele Frequency Aggregator	European	Sub	14286	G=0.75570	C=0.24430
Allele Frequency Aggregator	African	Sub	2946	G=0.9413	C=0.0587
Allele Frequency Aggregator	Other	Sub	692	G=0.834	C=0.166
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.839	C=0.161
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.829	C=0.171
Allele Frequency Aggregator	Asian	Sub	112	G=0.750	C=0.250
Allele Frequency Aggregator	South Asian	Sub	98	G=0.58	C=0.42
8.3KJPN	JAPANESE	Study-wide	16760	G=0.74093	C=0.25907
1000Genomes_30x	Global	Study-wide	6404	G=0.7894	C=0.2106
1000Genomes_30x	African	Sub	1786	G=0.9709	C=0.0291
1000Genomes_30x	Europe	Sub	1266	G=0.7757	C=0.2243
1000Genomes_30x	South Asian	Sub	1202	G=0.6281	C=0.3719
1000Genomes_30x	East Asian	Sub	1170	G=0.6444	C=0.3556
1000Genomes_30x	American	Sub	980	G=0.847	C=0.153
1000Genomes	Global	Study-wide	5008	G=0.7792	C=0.2208
1000Genomes	African	Sub	1322	G=0.9629	C=0.0371
1000Genomes	East Asian	Sub	1008	G=0.6538	C=0.3462
1000Genomes	Europe	Sub	1006	G=0.7763	C=0.2237
1000Genomes	South Asian	Sub	978	G=0.621	C=0.379
1000Genomes	American	Sub	694	G=0.839	C=0.161
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7179	C=0.2821
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7906	C=0.2094
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7732	C=0.2268
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.7382	C=0.2618
HapMap	Global	Study-wide	1890	G=0.8000	C=0.2000
HapMap	American	Sub	770	G=0.729	C=0.271
HapMap	African	Sub	690	G=0.887	C=0.113
HapMap	Asian	Sub	254	G=0.783	C=0.217
HapMap	Europe	Sub	176	G=0.795	C=0.205
Korean Genome Project	KOREAN	Study-wide	1832	G=0.7500	C=0.2500
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.759	C=0.241
Northern Sweden	ACPOP	Study-wide	600	G=0.793	C=0.207
SGDP_PRJ	Global	Study-wide	234	G=0.427	C=0.573
Qatari	Global	Study-wide	216	G=0.801	C=0.199
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.632	C=0.368
The Danish reference pan genome	Danish	Study-wide	40	G=0.68	C=0.33
Siberian	Global	Study-wide	26	G=0.42	C=0.58

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.96591950G>C
GRCh37.p13 chr 8	NC_000008.10:g.97604178G>C

Gene: SDC2, syndecan 2 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SDC2 transcript	NM_002998.4:c.61-1530G>C	N/A	Intron Variant
SDC2 transcript variant X1	XM_011517212.4:c.-27-1530… XM_011517212.4:c.-27-1530G>C	N/A	Intron Variant
SDC2 transcript variant X3	XM_024447228.2:c.-27-1530… XM_024447228.2:c.-27-1530G>C	N/A	Intron Variant
SDC2 transcript variant X2	XM_047422076.1:c.-27-1530… XM_047422076.1:c.-27-1530G>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	G=	C
GRCh38.p14 chr 8	NC_000008.11:g.96591950=	NC_000008.11:g.96591950G>C
GRCh37.p13 chr 8	NC_000008.10:g.97604178=	NC_000008.10:g.97604178G>C
SDC2 transcript	NM_002998.3:c.61-1530=	NM_002998.3:c.61-1530G>C
SDC2 transcript	NM_002998.4:c.61-1530=	NM_002998.4:c.61-1530G>C
SDC2 transcript variant X1	XM_005251019.1:c.34-1530=	XM_005251019.1:c.34-1530G>C
SDC2 transcript variant X2	XM_005251020.1:c.-27-1530=	XM_005251020.1:c.-27-1530G>C
SDC2 transcript variant X3	XM_005251021.1:c.-27-1530=	XM_005251021.1:c.-27-1530G>C
SDC2 transcript variant X1	XM_011517212.4:c.-27-1530=	XM_011517212.4:c.-27-1530G>C
SDC2 transcript variant X3	XM_024447228.2:c.-27-1530=	XM_024447228.2:c.-27-1530G>C
SDC2 transcript variant X2	XM_047422076.1:c.-27-1530=	XM_047422076.1:c.-27-1530G>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#.

67 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2936666	Apr 12, 2001 (94)
2	SC_JCM	ss3821588	Sep 28, 2001 (100)
3	CSHL-HAPMAP	ss17231535	Feb 27, 2004 (120)
4	PERLEGEN	ss24044023	Sep 20, 2004 (123)
5	ABI	ss44887264	Mar 14, 2006 (126)
6	AFFY	ss76536369	Dec 07, 2007 (129)
7	HUMANGENOME_JCVI	ss98096399	Feb 04, 2009 (130)
8	BGI	ss104554023	Dec 01, 2009 (131)
9	KRIBB_YJKIM	ss104860448	Feb 04, 2009 (130)
10	ENSEMBL	ss142808835	Dec 01, 2009 (131)
11	COMPLETE_GENOMICS	ss162621876	Jul 04, 2010 (132)
12	COMPLETE_GENOMICS	ss166912145	Jul 04, 2010 (132)
13	BUSHMAN	ss199516041	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss208677263	Jul 04, 2010 (132)
15	1000GENOMES	ss234548586	Jul 15, 2010 (132)
16	1000GENOMES	ss241379417	Jul 15, 2010 (132)
17	GMI	ss279923304	May 04, 2012 (137)
18	GMI	ss285890934	Apr 25, 2013 (138)
19	PJP	ss294146372	May 09, 2011 (134)
20	TISHKOFF	ss560933537	Apr 25, 2013 (138)
21	SSMP	ss655372420	Apr 25, 2013 (138)
22	EVA-GONL	ss985831315	Aug 21, 2014 (142)
23	JMKIDD_LAB	ss1075751629	Aug 21, 2014 (142)
24	1000GENOMES	ss1331065419	Aug 21, 2014 (142)
25	DDI	ss1431604488	Apr 01, 2015 (144)
26	EVA_GENOME_DK	ss1582801932	Apr 01, 2015 (144)
27	EVA_DECODE	ss1595439437	Apr 01, 2015 (144)
28	EVA_UK10K_ALSPAC	ss1621274674	Apr 01, 2015 (144)
29	EVA_UK10K_TWINSUK	ss1664268707	Apr 01, 2015 (144)
30	EVA_SVP	ss1713055880	Apr 01, 2015 (144)
31	WEILL_CORNELL_DGM	ss1929112673	Feb 12, 2016 (147)
32	GENOMED	ss1971046117	Jul 19, 2016 (147)
33	JJLAB	ss2025261176	Sep 14, 2016 (149)
34	ILLUMINA	ss2095213677	Dec 20, 2016 (150)
35	USC_VALOUEV	ss2153485677	Dec 20, 2016 (150)
36	HUMAN_LONGEVITY	ss2305642798	Dec 20, 2016 (150)
37	SYSTEMSBIOZJU	ss2627105536	Nov 08, 2017 (151)
38	GRF	ss2709263433	Nov 08, 2017 (151)
39	GNOMAD	ss2870265245	Nov 08, 2017 (151)
40	SWEGEN	ss3003662769	Nov 08, 2017 (151)
41	BIOINF_KMB_FNS_UNIBA	ss3026415074	Nov 08, 2017 (151)
42	CSHL	ss3348313166	Nov 08, 2017 (151)
43	URBANLAB	ss3648975042	Oct 12, 2018 (152)
44	ILLUMINA	ss3653411277	Oct 12, 2018 (152)
45	EGCUT_WGS	ss3671365796	Jul 13, 2019 (153)
46	EVA_DECODE	ss3722596729	Jul 13, 2019 (153)
47	ACPOP	ss3735920354	Jul 13, 2019 (153)
48	EVA	ss3768357328	Jul 13, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3811520194	Jul 13, 2019 (153)
50	EVA	ss3831308889	Apr 26, 2020 (154)
51	SGDP_PRJ	ss3870552580	Apr 26, 2020 (154)
52	KRGDB	ss3918115382	Apr 26, 2020 (154)
53	KOGIC	ss3964439716	Apr 26, 2020 (154)
54	TOPMED	ss4796787706	Apr 26, 2021 (155)
55	TOMMO_GENOMICS	ss5190048949	Apr 26, 2021 (155)
56	1000G_HIGH_COVERAGE	ss5278201182	Oct 16, 2022 (156)
57	EVA	ss5383090900	Oct 16, 2022 (156)
58	HUGCELL_USP	ss5474653658	Oct 16, 2022 (156)
59	EVA	ss5509472426	Oct 16, 2022 (156)
60	1000G_HIGH_COVERAGE	ss5569138826	Oct 16, 2022 (156)
61	SANFORD_IMAGENETICS	ss5645990674	Oct 16, 2022 (156)
62	TOMMO_GENOMICS	ss5732503096	Oct 16, 2022 (156)
63	YY_MCH	ss5809958967	Oct 16, 2022 (156)
64	EVA	ss5830938187	Oct 16, 2022 (156)
65	EVA	ss5856488664	Oct 16, 2022 (156)
66	EVA	ss5890176365	Oct 16, 2022 (156)
67	EVA	ss5975222545	Oct 16, 2022 (156)
68	1000Genomes	NC_000008.10 - 97604178	Oct 12, 2018 (152)
69	1000Genomes_30x	NC_000008.11 - 96591950	Oct 16, 2022 (156)
70	The Avon Longitudinal Study of Parents and Children	NC_000008.10 - 97604178	Oct 12, 2018 (152)
71	Genetic variation in the Estonian population	NC_000008.10 - 97604178	Oct 12, 2018 (152)
72	The Danish reference pan genome	NC_000008.10 - 97604178	Apr 26, 2020 (154)
73	gnomAD - Genomes	NC_000008.11 - 96591950	Apr 26, 2021 (155)
74	Genome of the Netherlands Release 5	NC_000008.10 - 97604178	Apr 26, 2020 (154)
75	HapMap	NC_000008.11 - 96591950	Apr 26, 2020 (154)
76	KOREAN population from KRGDB	NC_000008.10 - 97604178	Apr 26, 2020 (154)
77	Korean Genome Project	NC_000008.11 - 96591950	Apr 26, 2020 (154)
78	Northern Sweden	NC_000008.10 - 97604178	Jul 13, 2019 (153)
79	Qatari	NC_000008.10 - 97604178	Apr 26, 2020 (154)
80	SGDP_PRJ	NC_000008.10 - 97604178	Apr 26, 2020 (154)
81	Siberian	NC_000008.10 - 97604178	Apr 26, 2020 (154)
82	8.3KJPN	NC_000008.10 - 97604178	Apr 26, 2021 (155)
83	14KJPN	NC_000008.11 - 96591950	Oct 16, 2022 (156)
84	TopMed	NC_000008.11 - 96591950	Apr 26, 2021 (155)
85	UK 10K study - Twins	NC_000008.10 - 97604178	Oct 12, 2018 (152)
86	A Vietnamese Genetic Variation Database	NC_000008.10 - 97604178	Jul 13, 2019 (153)
87	ALFA	NC_000008.11 - 96591950	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss76536369, ss162621876, ss166912145, ss199516041, ss208677263, ss279923304, ss285890934, ss294146372, ss1595439437, ss1713055880	NC_000008.9:97673353:G:C	NC_000008.11:96591949:G:C	(self)
43233376, 24044378, 17104044, 8966870, 10732178, 25292776, 9205219, 11154603, 22569560, 6002031, 48018256, 24044378, 5345399, ss234548586, ss241379417, ss560933537, ss655372420, ss985831315, ss1075751629, ss1331065419, ss1431604488, ss1582801932, ss1621274674, ss1664268707, ss1929112673, ss1971046117, ss2025261176, ss2095213677, ss2153485677, ss2627105536, ss2709263433, ss2870265245, ss3003662769, ss3348313166, ss3653411277, ss3671365796, ss3735920354, ss3768357328, ss3831308889, ss3870552580, ss3918115382, ss5190048949, ss5383090900, ss5509472426, ss5645990674, ss5830938187, ss5975222545	NC_000008.10:97604177:G:C	NC_000008.11:96591949:G:C	(self)
56664761, 304928287, 3680083, 20817717, 66340200, 634165266, 1456231560, ss2305642798, ss3026415074, ss3648975042, ss3722596729, ss3811520194, ss3964439716, ss4796787706, ss5278201182, ss5474653658, ss5569138826, ss5732503096, ss5809958967, ss5856488664, ss5890176365	NC_000008.11:96591949:G:C	NC_000008.11:96591949:G:C	(self)
ss17231535	NT_008046.14:10822350:G:C	NC_000008.11:96591949:G:C	(self)
ss2936666, ss3821588, ss24044023, ss44887264, ss98096399, ss104554023, ss104860448, ss142808835	NT_008046.16:10877726:G:C	NC_000008.11:96591949:G: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 rs2028086

PMID	Title	Author	Year	Journal
18716610	Genomic screening identifies novel linkages and provides further evidence for a role of MYH9 in nonsyndromic cleft lip and palate.	Chiquet BT et al.	2009	European journal of human genetics

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

rs2028086