Name: rs2623587
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.

rs2623587

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr8:3698746 (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=0.143455 (37971/264690, TOPMED)
C=0.117809 (17555/149012, ALFA)
C=0.143131 (20065/140186, GnomAD) (+ 18 more)
C=0.01603 (453/28258, 14KJPN)
C=0.01521 (255/16760, 8.3KJPN)
C=0.1324 (848/6404, 1000G_30x)
C=0.1262 (632/5008, 1000G)
C=0.0859 (385/4480, Estonian)
C=0.1170 (451/3854, ALSPAC)
C=0.1259 (467/3708, TWINSUK)
C=0.0116 (34/2922, KOREAN)
C=0.1303 (246/1888, HapMap)
C=0.0109 (20/1832, Korea1K)
C=0.150 (150/998, GoNL)
C=0.112 (67/600, NorthernSweden)
C=0.102 (22/216, Qatari)
C=0.005 (1/216, Vietnamese)
A=0.415 (44/106, SGDP_PRJ)
C=0.07 (3/40, GENOME_DK)
A=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CSMD1 : 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	149012	A=0.882191	C=0.117809
European	Sub	125892	A=0.884345	C=0.115655
African	Sub	6208	A=0.7463	C=0.2537
African Others	Sub	220	A=0.718	C=0.282
African American	Sub	5988	A=0.7473	C=0.2527
Asian	Sub	670	A=0.984	C=0.016
East Asian	Sub	506	A=0.982	C=0.018
Other Asian	Sub	164	A=0.988	C=0.012
Latin American 1	Sub	878	A=0.825	C=0.175
Latin American 2	Sub	8396	A=0.9409	C=0.0591
South Asian	Sub	196	A=0.908	C=0.092
Other	Sub	6772	A=0.8906	C=0.1094

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	A=0.856545	C=0.143455
Allele Frequency Aggregator	Total	Global	149012	A=0.882191	C=0.117809
Allele Frequency Aggregator	European	Sub	125892	A=0.884345	C=0.115655
Allele Frequency Aggregator	Latin American 2	Sub	8396	A=0.9409	C=0.0591
Allele Frequency Aggregator	Other	Sub	6772	A=0.8906	C=0.1094
Allele Frequency Aggregator	African	Sub	6208	A=0.7463	C=0.2537
Allele Frequency Aggregator	Latin American 1	Sub	878	A=0.825	C=0.175
Allele Frequency Aggregator	Asian	Sub	670	A=0.984	C=0.016
Allele Frequency Aggregator	South Asian	Sub	196	A=0.908	C=0.092
gnomAD - Genomes	Global	Study-wide	140186	A=0.856869	C=0.143131
gnomAD - Genomes	European	Sub	75942	A=0.89121	C=0.10879
gnomAD - Genomes	African	Sub	41988	A=0.75514	C=0.24486
gnomAD - Genomes	American	Sub	13652	A=0.92301	C=0.07699
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.9531	C=0.0469
gnomAD - Genomes	East Asian	Sub	3130	A=0.9882	C=0.0118
gnomAD - Genomes	Other	Sub	2150	A=0.8707	C=0.1293
14KJPN	JAPANESE	Study-wide	28258	A=0.98397	C=0.01603
8.3KJPN	JAPANESE	Study-wide	16760	A=0.98479	C=0.01521
1000Genomes_30x	Global	Study-wide	6404	A=0.8676	C=0.1324
1000Genomes_30x	African	Sub	1786	A=0.7335	C=0.2665
1000Genomes_30x	Europe	Sub	1266	A=0.8870	C=0.1130
1000Genomes_30x	South Asian	Sub	1202	A=0.8735	C=0.1265
1000Genomes_30x	East Asian	Sub	1170	A=0.9932	C=0.0068
1000Genomes_30x	American	Sub	980	A=0.930	C=0.070
1000Genomes	Global	Study-wide	5008	A=0.8738	C=0.1262
1000Genomes	African	Sub	1322	A=0.7360	C=0.2640
1000Genomes	East Asian	Sub	1008	A=0.9921	C=0.0079
1000Genomes	Europe	Sub	1006	A=0.8936	C=0.1064
1000Genomes	South Asian	Sub	978	A=0.879	C=0.121
1000Genomes	American	Sub	694	A=0.928	C=0.072
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.9141	C=0.0859
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.8830	C=0.1170
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.8741	C=0.1259
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.9884	C=0.0116
HapMap	Global	Study-wide	1888	A=0.8697	C=0.1303
HapMap	American	Sub	768	A=0.895	C=0.105
HapMap	African	Sub	690	A=0.793	C=0.207
HapMap	Asian	Sub	254	A=0.992	C=0.008
HapMap	Europe	Sub	176	A=0.886	C=0.114
Korean Genome Project	KOREAN	Study-wide	1832	A=0.9891	C=0.0109
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.850	C=0.150
Northern Sweden	ACPOP	Study-wide	600	A=0.888	C=0.112
Qatari	Global	Study-wide	216	A=0.898	C=0.102
A Vietnamese Genetic Variation Database	Global	Study-wide	216	A=0.995	C=0.005
SGDP_PRJ	Global	Study-wide	106	A=0.415	C=0.585
The Danish reference pan genome	Danish	Study-wide	40	A=0.93	C=0.07
Siberian	Global	Study-wide	4	A=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 8	NC_000008.11:g.3698746A>C
GRCh37.p13 chr 8	NC_000008.10:g.3556268A>C

Gene: CSMD1, CUB and Sushi multiple domains 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CSMD1 transcript	NM_033225.6:c.1009+9668T>G	N/A	Intron Variant
CSMD1 transcript variant X1	XM_011534752.3:c.1009+966… XM_011534752.3:c.1009+9668T>G	N/A	Intron Variant
CSMD1 transcript variant X2	XM_017013731.2:c.1009+966… XM_017013731.2:c.1009+9668T>G	N/A	Intron Variant
CSMD1 transcript variant X3	XM_011534753.4:c.	N/A	Genic Upstream Transcript Variant
CSMD1 transcript variant X4	XM_011534754.2: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	A=	C
GRCh38.p14 chr 8	NC_000008.11:g.3698746=	NC_000008.11:g.3698746A>C
GRCh37.p13 chr 8	NC_000008.10:g.3556268=	NC_000008.10:g.3556268A>C
CSMD1 transcript	NM_033225.5:c.1009+9668=	NM_033225.5:c.1009+9668T>G
CSMD1 transcript	NM_033225.6:c.1009+9668=	NM_033225.6:c.1009+9668T>G
CSMD1 transcript variant X1	XM_011534752.3:c.1009+9668=	XM_011534752.3:c.1009+9668T>G
CSMD1 transcript variant X2	XM_017013731.2:c.1009+9668=	XM_017013731.2:c.1009+9668T>G

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#.

84 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3694207	Sep 28, 2001 (100)
2	PERLEGEN	ss23696044	Sep 20, 2004 (123)
3	ABI	ss44863339	Mar 14, 2006 (126)
4	AFFY	ss66274520	Jul 04, 2010 (132)
5	AFFY	ss75924940	Dec 07, 2007 (129)
6	KRIBB_YJKIM	ss81832020	Dec 15, 2007 (130)
7	1000GENOMES	ss112731327	Jan 25, 2009 (130)
8	ILLUMINA-UK	ss115827517	Feb 14, 2009 (130)
9	ILLUMINA	ss160564607	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss166060683	Jul 04, 2010 (132)
11	AFFY	ss169199797	Jul 04, 2010 (132)
12	BUSHMAN	ss198649034	Jul 04, 2010 (132)
13	BCM-HGSC-SUB	ss208584036	Jul 04, 2010 (132)
14	1000GENOMES	ss212158689	Jul 14, 2010 (132)
15	1000GENOMES	ss223481116	Jul 14, 2010 (132)
16	1000GENOMES	ss234274264	Jul 15, 2010 (132)
17	ILLUMINA	ss480620406	May 04, 2012 (137)
18	ILLUMINA	ss480635033	May 04, 2012 (137)
19	ILLUMINA	ss481472625	Sep 08, 2015 (146)
20	ILLUMINA	ss485105303	May 04, 2012 (137)
21	ILLUMINA	ss537110194	Sep 08, 2015 (146)
22	TISHKOFF	ss560477042	Apr 25, 2013 (138)
23	SSMP	ss654901066	Apr 25, 2013 (138)
24	ILLUMINA	ss778501627	Sep 08, 2015 (146)
25	ILLUMINA	ss782998937	Sep 08, 2015 (146)
26	ILLUMINA	ss783959486	Sep 08, 2015 (146)
27	ILLUMINA	ss832255970	Sep 08, 2015 (146)
28	ILLUMINA	ss833957754	Sep 08, 2015 (146)
29	EVA-GONL	ss985080486	Aug 21, 2014 (142)
30	JMKIDD_LAB	ss1075187629	Aug 21, 2014 (142)
31	1000GENOMES	ss1328191615	Aug 21, 2014 (142)
32	DDI	ss1431373578	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1582510197	Apr 01, 2015 (144)
34	EVA_DECODE	ss1594665997	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1619757577	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1662751610	Apr 01, 2015 (144)
37	EVA_SVP	ss1713006303	Apr 01, 2015 (144)
38	ILLUMINA	ss1752730099	Sep 08, 2015 (146)
39	HAMMER_LAB	ss1805349985	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1928358032	Feb 12, 2016 (147)
41	JJLAB	ss2024866899	Sep 14, 2016 (149)
42	USC_VALOUEV	ss2153097337	Dec 20, 2016 (150)
43	HUMAN_LONGEVITY	ss2299902618	Dec 20, 2016 (150)
44	ILLUMINA	ss2634695431	Nov 08, 2017 (151)
45	GNOMAD	ss2862080314	Nov 08, 2017 (151)
46	AFFY	ss2986063816	Nov 08, 2017 (151)
47	SWEGEN	ss3002490020	Nov 08, 2017 (151)
48	BIOINF_KMB_FNS_UNIBA	ss3026222402	Nov 08, 2017 (151)
49	CSHL	ss3347985490	Nov 08, 2017 (151)
50	ILLUMINA	ss3629974170	Oct 12, 2018 (152)
51	ILLUMINA	ss3632597624	Oct 12, 2018 (152)
52	ILLUMINA	ss3633486809	Oct 12, 2018 (152)
53	ILLUMINA	ss3634212961	Oct 12, 2018 (152)
54	ILLUMINA	ss3635153918	Oct 12, 2018 (152)
55	ILLUMINA	ss3635892126	Oct 12, 2018 (152)
56	ILLUMINA	ss3636889427	Oct 12, 2018 (152)
57	ILLUMINA	ss3637645218	Oct 12, 2018 (152)
58	ILLUMINA	ss3640861208	Oct 12, 2018 (152)
59	EGCUT_WGS	ss3670203258	Jul 13, 2019 (153)
60	EVA_DECODE	ss3721214734	Jul 13, 2019 (153)
61	ACPOP	ss3735306444	Jul 13, 2019 (153)
62	ILLUMINA	ss3745453808	Jul 13, 2019 (153)
63	EVA	ss3767489766	Jul 13, 2019 (153)
64	ILLUMINA	ss3772946459	Jul 13, 2019 (153)
65	KHV_HUMAN_GENOMES	ss3810653965	Jul 13, 2019 (153)
66	EVA	ss3838981890	Apr 26, 2020 (154)
67	EVA	ss3844440025	Apr 26, 2020 (154)
68	SGDP_PRJ	ss3869009019	Apr 26, 2020 (154)
69	KRGDB	ss3916429585	Apr 26, 2020 (154)
70	KOGIC	ss3963063936	Apr 26, 2020 (154)
71	EVA	ss4017371762	Apr 26, 2021 (155)
72	TOPMED	ss4772430162	Apr 26, 2021 (155)
73	TOMMO_GENOMICS	ss5186826384	Apr 26, 2021 (155)
74	1000G_HIGH_COVERAGE	ss5275697237	Oct 14, 2022 (156)
75	EVA	ss5315300455	Oct 14, 2022 (156)
76	EVA	ss5378495310	Oct 14, 2022 (156)
77	HUGCELL_USP	ss5472436992	Oct 14, 2022 (156)
78	1000G_HIGH_COVERAGE	ss5565287600	Oct 14, 2022 (156)
79	SANFORD_IMAGENETICS	ss5644540521	Oct 14, 2022 (156)
80	TOMMO_GENOMICS	ss5728217270	Oct 14, 2022 (156)
81	EVA	ss5799744490	Oct 14, 2022 (156)
82	EVA	ss5829976058	Oct 14, 2022 (156)
83	EVA	ss5887328436	Oct 14, 2022 (156)
84	EVA	ss5973732824	Oct 14, 2022 (156)
85	1000Genomes	NC_000008.10 - 3556268	Oct 12, 2018 (152)
86	1000Genomes_30x	NC_000008.11 - 3698746	Oct 14, 2022 (156)
87	The Avon Longitudinal Study of Parents and Children	NC_000008.10 - 3556268	Oct 12, 2018 (152)
88	Genetic variation in the Estonian population	NC_000008.10 - 3556268	Oct 12, 2018 (152)
89	The Danish reference pan genome	NC_000008.10 - 3556268	Apr 26, 2020 (154)
90	gnomAD - Genomes	NC_000008.11 - 3698746	Apr 26, 2021 (155)
91	Genome of the Netherlands Release 5	NC_000008.10 - 3556268	Apr 26, 2020 (154)
92	HapMap	NC_000008.11 - 3698746	Apr 26, 2020 (154)
93	KOREAN population from KRGDB	NC_000008.10 - 3556268	Apr 26, 2020 (154)
94	Korean Genome Project	NC_000008.11 - 3698746	Apr 26, 2020 (154)
95	Northern Sweden	NC_000008.10 - 3556268	Jul 13, 2019 (153)
96	Qatari	NC_000008.10 - 3556268	Apr 26, 2020 (154)
97	SGDP_PRJ	NC_000008.10 - 3556268	Apr 26, 2020 (154)
98	Siberian	NC_000008.10 - 3556268	Apr 26, 2020 (154)
99	8.3KJPN	NC_000008.10 - 3556268	Apr 26, 2021 (155)
100	14KJPN	NC_000008.11 - 3698746	Oct 14, 2022 (156)
101	TopMed	NC_000008.11 - 3698746	Apr 26, 2021 (155)
102	UK 10K study - Twins	NC_000008.10 - 3556268	Oct 12, 2018 (152)
103	A Vietnamese Genetic Variation Database	NC_000008.10 - 3556268	Jul 13, 2019 (153)
104	ALFA	NC_000008.11 - 3698746	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).

Associated ID	History Updated (Build)
rs60296062	Feb 27, 2009 (130)
rs386570748	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss112731327, ss115827517, ss160564607, ss166060683, ss198649034, ss208584036, ss212158689, ss480620406, ss1594665997, ss1713006303	NC_000008.9:3543675:A:C	NC_000008.11:3698745:A:C	(self)
40271237, 22394931, 15941506, 8675135, 10000109, 23606979, 8591309, 10399962, 21025999, 5613691, 44795691, 22394931, 4986492, ss223481116, ss234274264, ss480635033, ss481472625, ss485105303, ss537110194, ss560477042, ss654901066, ss778501627, ss782998937, ss783959486, ss832255970, ss833957754, ss985080486, ss1075187629, ss1328191615, ss1431373578, ss1582510197, ss1619757577, ss1662751610, ss1752730099, ss1805349985, ss1928358032, ss2024866899, ss2153097337, ss2634695431, ss2862080314, ss2986063816, ss3002490020, ss3347985490, ss3629974170, ss3632597624, ss3633486809, ss3634212961, ss3635153918, ss3635892126, ss3636889427, ss3637645218, ss3640861208, ss3670203258, ss3735306444, ss3745453808, ss3767489766, ss3772946459, ss3838981890, ss3869009019, ss3916429585, ss4017371762, ss5186826384, ss5315300455, ss5378495310, ss5644540521, ss5799744490, ss5829976058, ss5973732824	NC_000008.10:3556267:A:C	NC_000008.11:3698745:A:C	(self)
52813535, 284165674, 3542671, 19441937, 62054374, 609807722, 10031056226, ss2299902618, ss3026222402, ss3721214734, ss3810653965, ss3844440025, ss3963063936, ss4772430162, ss5275697237, ss5472436992, ss5565287600, ss5728217270, ss5887328436	NC_000008.11:3698745:A:C	NC_000008.11:3698745:A:C	(self)
ss3694207, ss23696044, ss44863339, ss75924940, ss81832020, ss169199797	NT_023736.17:3546267:A:C	NC_000008.11:3698745:A:C	(self)
ss66274520	NT_023736.18:3638745:A:C	NC_000008.11:3698745: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 rs2623587

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

rs2623587