Name: rs2205088
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.

rs2205088

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr21:40430572 (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: C>A / C>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.189006 (50028/264690, TOPMED)
A=0.29553 (8351/28258, 14KJPN)
A=0.08928 (1531/17148, ALFA) (+ 14 more)
A=0.29368 (4922/16760, 8.3KJPN)
A=0.2183 (1398/6404, 1000G_30x)
A=0.2185 (1094/5008, 1000G)
A=0.1670 (748/4480, Estonian)
A=0.2570 (753/2930, KOREAN)
A=0.2587 (474/1832, Korea1K)
A=0.1952 (221/1132, Daghestan)
A=0.143 (143/998, GoNL)
A=0.200 (120/600, NorthernSweden)
C=0.382 (91/238, SGDP_PRJ)
A=0.134 (29/216, Qatari)
A=0.201 (43/214, Vietnamese)
A=0.12 (5/40, GENOME_DK)
C=0.45 (10/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DSCAM : 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	17148	C=0.91072	A=0.08928, G=0.00000
European	Sub	11696	C=0.93331	A=0.06669, G=0.00000
African	Sub	4202	C=0.8282	A=0.1718, G=0.0000
African Others	Sub	136	C=0.816	A=0.184, G=0.000
African American	Sub	4066	C=0.8286	A=0.1714, G=0.0000
Asian	Sub	74	C=0.99	A=0.01, G=0.00
East Asian	Sub	54	C=0.98	A=0.02, G=0.00
Other Asian	Sub	20	C=1.00	A=0.00, G=0.00
Latin American 1	Sub	96	C=1.00	A=0.00, G=0.00
Latin American 2	Sub	456	C=1.000	A=0.000, G=0.000
South Asian	Sub	52	C=0.98	A=0.02, G=0.00
Other	Sub	572	C=0.953	A=0.047, G=0.000

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	C=0.810994	A=0.189006
14KJPN	JAPANESE	Study-wide	28258	C=0.70447	A=0.29553
Allele Frequency Aggregator	Total	Global	17148	C=0.91072	A=0.08928, G=0.00000
Allele Frequency Aggregator	European	Sub	11696	C=0.93331	A=0.06669, G=0.00000
Allele Frequency Aggregator	African	Sub	4202	C=0.8282	A=0.1718, G=0.0000
Allele Frequency Aggregator	Other	Sub	572	C=0.953	A=0.047, G=0.000
Allele Frequency Aggregator	Latin American 2	Sub	456	C=1.000	A=0.000, G=0.000
Allele Frequency Aggregator	Latin American 1	Sub	96	C=1.00	A=0.00, G=0.00
Allele Frequency Aggregator	Asian	Sub	74	C=0.99	A=0.01, G=0.00
Allele Frequency Aggregator	South Asian	Sub	52	C=0.98	A=0.02, G=0.00
8.3KJPN	JAPANESE	Study-wide	16760	C=0.70632	A=0.29368
1000Genomes_30x	Global	Study-wide	6404	C=0.7817	A=0.2183
1000Genomes_30x	African	Sub	1786	C=0.7228	A=0.2772
1000Genomes_30x	Europe	Sub	1266	C=0.8420	A=0.1580
1000Genomes_30x	South Asian	Sub	1202	C=0.7604	A=0.2396
1000Genomes_30x	East Asian	Sub	1170	C=0.7590	A=0.2410
1000Genomes_30x	American	Sub	980	C=0.864	A=0.136
1000Genomes	Global	Study-wide	5008	C=0.7815	A=0.2185
1000Genomes	African	Sub	1322	C=0.7352	A=0.2648
1000Genomes	East Asian	Sub	1008	C=0.7569	A=0.2431
1000Genomes	Europe	Sub	1006	C=0.8380	A=0.1620
1000Genomes	South Asian	Sub	978	C=0.753	A=0.247
1000Genomes	American	Sub	694	C=0.865	A=0.135
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8330	A=0.1670
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.7430	A=0.2570
Korean Genome Project	KOREAN	Study-wide	1832	C=0.7413	A=0.2587
Genome-wide autozygosity in Daghestan	Global	Study-wide	1132	C=0.8048	A=0.1952
Genome-wide autozygosity in Daghestan	Daghestan	Sub	626	C=0.834	A=0.166
Genome-wide autozygosity in Daghestan	Near_East	Sub	144	C=0.792	A=0.208
Genome-wide autozygosity in Daghestan	Central Asia	Sub	120	C=0.775	A=0.225
Genome-wide autozygosity in Daghestan	Europe	Sub	108	C=0.861	A=0.139
Genome-wide autozygosity in Daghestan	South Asian	Sub	98	C=0.63	A=0.37
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	C=0.75	A=0.25
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.857	A=0.143
Northern Sweden	ACPOP	Study-wide	600	C=0.800	A=0.200
SGDP_PRJ	Global	Study-wide	238	C=0.382	A=0.618
Qatari	Global	Study-wide	216	C=0.866	A=0.134
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.799	A=0.201
The Danish reference pan genome	Danish	Study-wide	40	C=0.88	A=0.12
Siberian	Global	Study-wide	22	C=0.45	A=0.55

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 21	NC_000021.9:g.40430572C>A
GRCh38.p14 chr 21	NC_000021.9:g.40430572C>G
GRCh37.p13 chr 21	NC_000021.8:g.41802499C>A
GRCh37.p13 chr 21	NC_000021.8:g.41802499C>G
GRCh38.p14 chr 21 fix patch HG2265_PATCH	NW_025791814.1:g.570226C>A
GRCh38.p14 chr 21 fix patch HG2265_PATCH	NW_025791814.1:g.570226C>G

Gene: DSCAM, DS cell adhesion molecule (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DSCAM transcript variant 2	NM_001271534.3:c.509-6132… NM_001271534.3:c.509-61327G>T	N/A	Intron Variant
DSCAM transcript variant 1	NM_001389.5:c.509-61327G>T	N/A	Intron Variant
DSCAM transcript variant 3	NR_073202.3:n.	N/A	Intron Variant
DSCAM transcript variant X1	XM_017028281.2:c.	N/A	Genic Upstream Transcript 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	C=	A	G
GRCh38.p14 chr 21	NC_000021.9:g.40430572=	NC_000021.9:g.40430572C>A	NC_000021.9:g.40430572C>G
GRCh37.p13 chr 21	NC_000021.8:g.41802499=	NC_000021.8:g.41802499C>A	NC_000021.8:g.41802499C>G
GRCh38.p14 chr 21 fix patch HG2265_PATCH	NW_025791814.1:g.570226=	NW_025791814.1:g.570226C>A	NW_025791814.1:g.570226C>G
DSCAM transcript variant 2	NM_001271534.1:c.509-61327=	NM_001271534.1:c.509-61327G>T	NM_001271534.1:c.509-61327G>C
DSCAM transcript variant 2	NM_001271534.3:c.509-61327=	NM_001271534.3:c.509-61327G>T	NM_001271534.3:c.509-61327G>C
DSCAM transcript variant 1	NM_001389.3:c.509-61327=	NM_001389.3:c.509-61327G>T	NM_001389.3:c.509-61327G>C
DSCAM transcript variant 1	NM_001389.5:c.509-61327=	NM_001389.5:c.509-61327G>T	NM_001389.5:c.509-61327G>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#.

60 SubSNP, 23 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss3146101	Jun 15, 2001 (96)
2	WI_SSAHASNP	ss12501130	Jul 11, 2003 (116)
3	ABI	ss41457997	Mar 13, 2006 (126)
4	1000GENOMES	ss112488754	Jan 25, 2009 (130)
5	COMPLETE_GENOMICS	ss168067959	Jul 04, 2010 (132)
6	COMPLETE_GENOMICS	ss172054785	Jul 04, 2010 (132)
7	BUSHMAN	ss204023098	Jul 04, 2010 (132)
8	1000GENOMES	ss228575780	Jul 14, 2010 (132)
9	1000GENOMES	ss237990172	Jul 15, 2010 (132)
10	1000GENOMES	ss244127341	Jul 15, 2010 (132)
11	GMI	ss283549632	May 04, 2012 (137)
12	GMI	ss287534695	Apr 25, 2013 (138)
13	TISHKOFF	ss566508961	Apr 25, 2013 (138)
14	SSMP	ss662419684	Apr 25, 2013 (138)
15	EVA-GONL	ss995139641	Aug 21, 2014 (142)
16	JMKIDD_LAB	ss1082515858	Aug 21, 2014 (142)
17	1000GENOMES	ss1366368780	Aug 21, 2014 (142)
18	HAMMER_LAB	ss1397780981	Sep 08, 2015 (146)
19	DDI	ss1429190931	Apr 01, 2015 (144)
20	EVA_GENOME_DK	ss1579671432	Apr 01, 2015 (144)
21	EVA_UK10K_ALSPAC	ss1639605510	Apr 01, 2015 (144)
22	EVA_UK10K_ALSPAC	ss1639605511	Apr 01, 2015 (144)
23	EVA_UK10K_TWINSUK	ss1682599543	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1682599544	Apr 01, 2015 (144)
25	EVA_DECODE	ss1699211119	Apr 01, 2015 (144)
26	HAMMER_LAB	ss1809697034	Sep 08, 2015 (146)
27	WEILL_CORNELL_DGM	ss1938689668	Feb 12, 2016 (147)
28	GENOMED	ss1969230361	Jul 19, 2016 (147)
29	JJLAB	ss2030117964	Sep 14, 2016 (149)
30	USC_VALOUEV	ss2158722993	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2245940901	Dec 20, 2016 (150)
32	SYSTEMSBIOZJU	ss2629558423	Nov 08, 2017 (151)
33	GRF	ss2704454145	Nov 08, 2017 (151)
34	GNOMAD	ss2972020952	Nov 08, 2017 (151)
35	AFFY	ss2985847813	Nov 08, 2017 (151)
36	SWEGEN	ss3018925735	Nov 08, 2017 (151)
37	BIOINF_KMB_FNS_UNIBA	ss3028898348	Nov 08, 2017 (151)
38	CSHL	ss3352728549	Nov 08, 2017 (151)
39	EGCUT_WGS	ss3685502947	Jul 13, 2019 (153)
40	EVA_DECODE	ss3707773018	Jul 13, 2019 (153)
41	ACPOP	ss3743750484	Jul 13, 2019 (153)
42	EVA	ss3759132816	Jul 13, 2019 (153)
43	KHV_HUMAN_GENOMES	ss3822299679	Jul 13, 2019 (153)
44	EVA	ss3835885370	Apr 27, 2020 (154)
45	SGDP_PRJ	ss3890045658	Apr 27, 2020 (154)
46	KRGDB	ss3940390869	Apr 27, 2020 (154)
47	KOGIC	ss3983134267	Apr 27, 2020 (154)
48	TOPMED	ss5102320088	Apr 27, 2021 (155)
49	TOMMO_GENOMICS	ss5231622929	Apr 27, 2021 (155)
50	1000G_HIGH_COVERAGE	ss5310290243	Oct 16, 2022 (156)
51	EVA	ss5440019204	Oct 16, 2022 (156)
52	HUGCELL_USP	ss5502331208	Oct 16, 2022 (156)
53	1000G_HIGH_COVERAGE	ss5617466420	Oct 16, 2022 (156)
54	SANFORD_IMAGENETICS	ss5664055917	Oct 16, 2022 (156)
55	TOMMO_GENOMICS	ss5792161396	Oct 16, 2022 (156)
56	YY_MCH	ss5818462103	Oct 16, 2022 (156)
57	EVA	ss5839069612	Oct 16, 2022 (156)
58	EVA	ss5853314693	Oct 16, 2022 (156)
59	EVA	ss5892439854	Oct 16, 2022 (156)
60	EVA	ss5958953416	Oct 16, 2022 (156)
61	1000Genomes	NC_000021.8 - 41802499	Oct 12, 2018 (152)
62	1000Genomes_30x	NC_000021.9 - 40430572	Oct 16, 2022 (156)
63	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 44217752 (NC_000021.8:41802498:C:C 3264/3854, NC_000021.8:41802498:C:A 590/3854) Row 44217753 (NC_000021.8:41802498:C:C 3853/3854, NC_000021.8:41802498:C:G 1/3854)	-	Oct 12, 2018 (152)
64	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 44217752 (NC_000021.8:41802498:C:C 3264/3854, NC_000021.8:41802498:C:A 590/3854) Row 44217753 (NC_000021.8:41802498:C:C 3853/3854, NC_000021.8:41802498:C:G 1/3854)	-	Oct 12, 2018 (152)
65	Genome-wide autozygosity in Daghestan	NC_000021.7 - 40724369	Apr 27, 2020 (154)
66	Genetic variation in the Estonian population	NC_000021.8 - 41802499	Oct 12, 2018 (152)
67	The Danish reference pan genome	NC_000021.8 - 41802499	Apr 27, 2020 (154)
68	gnomAD - Genomes Submission ignored due to conflicting rows: Row 563763120 (NC_000021.9:40430571:C:A 26903/140062) Row 563763121 (NC_000021.9:40430571:C:G 2/140100)	-	Apr 27, 2021 (155)
69	gnomAD - Genomes Submission ignored due to conflicting rows: Row 563763120 (NC_000021.9:40430571:C:A 26903/140062) Row 563763121 (NC_000021.9:40430571:C:G 2/140100)	-	Apr 27, 2021 (155)
70	Genome of the Netherlands Release 5	NC_000021.8 - 41802499	Apr 27, 2020 (154)
71	KOREAN population from KRGDB	NC_000021.8 - 41802499	Apr 27, 2020 (154)
72	Korean Genome Project	NC_000021.9 - 40430572	Apr 27, 2020 (154)
73	Northern Sweden	NC_000021.8 - 41802499	Jul 13, 2019 (153)
74	Qatari	NC_000021.8 - 41802499	Apr 27, 2020 (154)
75	SGDP_PRJ	NC_000021.8 - 41802499	Apr 27, 2020 (154)
76	Siberian	NC_000021.8 - 41802499	Apr 27, 2020 (154)
77	8.3KJPN	NC_000021.8 - 41802499	Apr 27, 2021 (155)
78	14KJPN	NC_000021.9 - 40430572	Oct 16, 2022 (156)
79	TopMed	NC_000021.9 - 40430572	Apr 27, 2021 (155)
80	UK 10K study - Twins Submission ignored due to conflicting rows: Row 44217752 (NC_000021.8:41802498:C:C 3160/3708, NC_000021.8:41802498:C:A 548/3708) Row 44217753 (NC_000021.8:41802498:C:C 3708/3708, NC_000021.8:41802498:C:G 0/3708)	-	Oct 12, 2018 (152)
81	UK 10K study - Twins Submission ignored due to conflicting rows: Row 44217752 (NC_000021.8:41802498:C:C 3160/3708, NC_000021.8:41802498:C:A 548/3708) Row 44217753 (NC_000021.8:41802498:C:C 3708/3708, NC_000021.8:41802498:C:G 0/3708)	-	Oct 12, 2018 (152)
82	A Vietnamese Genetic Variation Database	NC_000021.8 - 41802499	Jul 13, 2019 (153)
83	ALFA	NC_000021.9 - 40430572	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
294990, ss112488754, ss168067959, ss172054785, ss204023098, ss283549632, ss287534695, ss1397780981, ss1699211119	NC_000021.7:40724368:C:A	NC_000021.9:40430571:C:A	(self)
79891838, 31241195, 5836371, 19696991, 47568263, 17035349, 20731590, 42062638, 11239347, 89592236, 9756588, ss228575780, ss237990172, ss244127341, ss566508961, ss662419684, ss995139641, ss1082515858, ss1366368780, ss1429190931, ss1579671432, ss1639605510, ss1682599543, ss1809697034, ss1938689668, ss1969230361, ss2030117964, ss2158722993, ss2629558423, ss2704454145, ss2972020952, ss2985847813, ss3018925735, ss3352728549, ss3685502947, ss3743750484, ss3759132816, ss3835885370, ss3890045658, ss3940390869, ss5231622929, ss5440019204, ss5664055917, ss5839069612, ss5958953416	NC_000021.8:41802498:C:A	NC_000021.9:40430571:C:A	(self)
104992355, 39512268, 125998500, 377429034, 1530906120, ss2245940901, ss3028898348, ss3707773018, ss3822299679, ss3983134267, ss5102320088, ss5310290243, ss5502331208, ss5617466420, ss5792161396, ss5818462103, ss5853314693, ss5892439854	NC_000021.9:40430571:C:A	NC_000021.9:40430571:C:A	(self)
ss12501130	NT_011512.8:27463334:C:A	NC_000021.9:40430571:C:A	(self)
ss3146101, ss41457997	NT_011512.11:27464369:C:A	NC_000021.9:40430571:C:A	(self)
ss1639605511, ss1682599544	NC_000021.8:41802498:C:G	NC_000021.9:40430571:C:G	(self)
1530906120	NC_000021.9:40430571:C:G	NC_000021.9:40430571:C: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 rs2205088

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

rs2205088