Name: rs3775141
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.

rs3775141

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:789442 (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: A=0.448249 (118647/264690, TOPMED)
A=0.451340 (63211/140052, GnomAD)
C=0.25175 (7114/28258, 14KJPN) (+ 16 more)
A=0.47141 (8905/18890, ALFA)
C=0.25107 (4208/16760, 8.3KJPN)
A=0.4785 (3064/6404, 1000G_30x)
A=0.4866 (2437/5008, 1000G)
C=0.4212 (1887/4480, Estonian)
A=0.4357 (1679/3854, ALSPAC)
A=0.4288 (1590/3708, TWINSUK)
C=0.3345 (980/2930, KOREAN)
C=0.3117 (571/1832, Korea1K)
A=0.465 (464/998, GoNL)
A=0.468 (281/600, NorthernSweden)
A=0.324 (120/370, SGDP_PRJ)
A=0.333 (72/216, Qatari)
C=0.434 (92/212, Vietnamese)
A=0.40 (16/40, GENOME_DK)
A=0.41 (14/34, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CPLX1 : Intron Variant
LOC105374339 : 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	18890	A=0.47141	C=0.52859
European	Sub	14286	A=0.48607	C=0.51393
African	Sub	2946	A=0.3975	C=0.6025
African Others	Sub	114	A=0.412	C=0.588
African American	Sub	2832	A=0.3969	C=0.6031
Asian	Sub	112	A=0.554	C=0.446
East Asian	Sub	86	A=0.62	C=0.38
Other Asian	Sub	26	A=0.35	C=0.65
Latin American 1	Sub	146	A=0.425	C=0.575
Latin American 2	Sub	610	A=0.538	C=0.462
South Asian	Sub	98	A=0.42	C=0.58
Other	Sub	692	A=0.429	C=0.571

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	A=0.448249	C=0.551751
gnomAD - Genomes	Global	Study-wide	140052	A=0.451340	C=0.548660
gnomAD - Genomes	European	Sub	75844	A=0.46219	C=0.53781
gnomAD - Genomes	African	Sub	41974	A=0.39501	C=0.60499
gnomAD - Genomes	American	Sub	13638	A=0.53278	C=0.46722
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.4404	C=0.5596
gnomAD - Genomes	East Asian	Sub	3124	A=0.6028	C=0.3972
gnomAD - Genomes	Other	Sub	2150	A=0.4488	C=0.5512
14KJPN	JAPANESE	Study-wide	28258	A=0.74825	C=0.25175
Allele Frequency Aggregator	Total	Global	18890	A=0.47141	C=0.52859
Allele Frequency Aggregator	European	Sub	14286	A=0.48607	C=0.51393
Allele Frequency Aggregator	African	Sub	2946	A=0.3975	C=0.6025
Allele Frequency Aggregator	Other	Sub	692	A=0.429	C=0.571
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.538	C=0.462
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.425	C=0.575
Allele Frequency Aggregator	Asian	Sub	112	A=0.554	C=0.446
Allele Frequency Aggregator	South Asian	Sub	98	A=0.42	C=0.58
8.3KJPN	JAPANESE	Study-wide	16760	A=0.74893	C=0.25107
1000Genomes_30x	Global	Study-wide	6404	A=0.4785	C=0.5215
1000Genomes_30x	African	Sub	1786	A=0.3841	C=0.6159
1000Genomes_30x	Europe	Sub	1266	A=0.4415	C=0.5585
1000Genomes_30x	South Asian	Sub	1202	A=0.4692	C=0.5308
1000Genomes_30x	East Asian	Sub	1170	A=0.5974	C=0.4026
1000Genomes_30x	American	Sub	980	A=0.567	C=0.433
1000Genomes	Global	Study-wide	5008	A=0.4866	C=0.5134
1000Genomes	African	Sub	1322	A=0.3964	C=0.6036
1000Genomes	East Asian	Sub	1008	A=0.6091	C=0.3909
1000Genomes	Europe	Sub	1006	A=0.4384	C=0.5616
1000Genomes	South Asian	Sub	978	A=0.481	C=0.519
1000Genomes	American	Sub	694	A=0.559	C=0.441
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5788	C=0.4212
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.4357	C=0.5643
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.4288	C=0.5712
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.6655	C=0.3345
Korean Genome Project	KOREAN	Study-wide	1832	A=0.6883	C=0.3117
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.465	C=0.535
Northern Sweden	ACPOP	Study-wide	600	A=0.468	C=0.532
SGDP_PRJ	Global	Study-wide	370	A=0.324	C=0.676
Qatari	Global	Study-wide	216	A=0.333	C=0.667
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.566	C=0.434
The Danish reference pan genome	Danish	Study-wide	40	A=0.40	C=0.60
Siberian	Global	Study-wide	34	A=0.41	C=0.59

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 4	NC_000004.12:g.789442A>C
GRCh37.p13 chr 4	NC_000004.11:g.783230A>C

Gene: CPLX1, complexin 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CPLX1 transcript	NM_006651.4:c.208-2744T>G	N/A	Intron Variant
CPLX1 transcript variant X1	XM_011513391.2:c.163-2744… XM_011513391.2:c.163-2744T>G	N/A	Intron Variant

Gene: LOC105374339, uncharacterized LOC105374339 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105374339 transcript variant X1	XR_925031.4:n.	N/A	Intron Variant
LOC105374339 transcript variant X2	XR_925032.4:n.	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	A=	C
GRCh38.p14 chr 4	NC_000004.12:g.789442=	NC_000004.12:g.789442A>C
GRCh37.p13 chr 4	NC_000004.11:g.783230=	NC_000004.11:g.783230A>C
CPLX1 transcript	NM_006651.3:c.208-2744=	NM_006651.3:c.208-2744T>G
CPLX1 transcript	NM_006651.4:c.208-2744=	NM_006651.4:c.208-2744T>G
CPLX1 transcript variant X2	XM_005272258.1:c.163-2744=	XM_005272258.1:c.163-2744T>G
CPLX1 transcript variant X1	XM_011513391.2:c.163-2744=	XM_011513391.2:c.163-2744T>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#.

71 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	YUSUKE	ss4961207	Aug 28, 2002 (107)
2	BCM_SSAHASNP	ss10111986	Jul 11, 2003 (116)
3	CSHL-HAPMAP	ss16996332	Feb 27, 2004 (120)
4	ABI	ss44564485	Mar 15, 2006 (126)
5	HGSV	ss77176318	Dec 06, 2007 (129)
6	HGSV	ss84362008	Dec 15, 2007 (130)
7	BCMHGSC_JDW	ss92436869	Mar 24, 2008 (129)
8	BGI	ss104031647	Dec 01, 2009 (131)
9	1000GENOMES	ss112842085	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss116835082	Feb 14, 2009 (130)
11	ENSEMBL	ss134635180	Dec 01, 2009 (131)
12	ENSEMBL	ss139391251	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss161886470	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss165986977	Jul 04, 2010 (132)
15	BUSHMAN	ss197886712	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss206332102	Jul 04, 2010 (132)
17	1000GENOMES	ss211342513	Jul 14, 2010 (132)
18	1000GENOMES	ss220689826	Jul 14, 2010 (132)
19	1000GENOMES	ss232222468	Jul 14, 2010 (132)
20	1000GENOMES	ss239551871	Jul 15, 2010 (132)
21	GMI	ss277536690	May 04, 2012 (137)
22	GMI	ss284828350	Apr 25, 2013 (138)
23	PJP	ss293052674	May 09, 2011 (134)
24	TISHKOFF	ss557249242	Apr 25, 2013 (138)
25	SSMP	ss651001719	Apr 25, 2013 (138)
26	EVA-GONL	ss979665218	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1071210584	Aug 21, 2014 (142)
28	1000GENOMES	ss1308057521	Aug 21, 2014 (142)
29	DDI	ss1429737191	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1580377621	Apr 01, 2015 (144)
31	EVA_DECODE	ss1589162157	Apr 01, 2015 (144)
32	EVA_UK10K_ALSPAC	ss1609221398	Apr 01, 2015 (144)
33	EVA_UK10K_TWINSUK	ss1652215431	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1800780193	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1922895210	Feb 12, 2016 (147)
36	GENOMED	ss1969636166	Jul 19, 2016 (147)
37	JJLAB	ss2022021781	Sep 14, 2016 (149)
38	USC_VALOUEV	ss2150126854	Dec 20, 2016 (150)
39	HUMAN_LONGEVITY	ss2259759828	Dec 20, 2016 (150)
40	SYSTEMSBIOZJU	ss2625511638	Nov 08, 2017 (151)
41	GRF	ss2705561440	Nov 08, 2017 (151)
42	GNOMAD	ss2804599039	Nov 08, 2017 (151)
43	SWEGEN	ss2993979835	Nov 08, 2017 (151)
44	BIOINF_KMB_FNS_UNIBA	ss3024780547	Nov 08, 2017 (151)
45	CSHL	ss3345494422	Nov 08, 2017 (151)
46	URBANLAB	ss3647631141	Oct 12, 2018 (152)
47	EGCUT_WGS	ss3661918974	Jul 13, 2019 (153)
48	EVA_DECODE	ss3711220489	Jul 13, 2019 (153)
49	ACPOP	ss3730771456	Jul 13, 2019 (153)
50	EVA	ss3761274556	Jul 13, 2019 (153)
51	KHV_HUMAN_GENOMES	ss3804415588	Jul 13, 2019 (153)
52	EVA	ss3828322402	Apr 25, 2020 (154)
53	EVA	ss3837592402	Apr 25, 2020 (154)
54	EVA	ss3843025653	Apr 25, 2020 (154)
55	SGDP_PRJ	ss3858004922	Apr 25, 2020 (154)
56	KRGDB	ss3904127756	Apr 25, 2020 (154)
57	KOGIC	ss3953335670	Apr 25, 2020 (154)
58	TOPMED	ss4599925592	Apr 26, 2021 (155)
59	TOMMO_GENOMICS	ss5163779007	Apr 26, 2021 (155)
60	1000G_HIGH_COVERAGE	ss5257713919	Oct 17, 2022 (156)
61	EVA	ss5346321452	Oct 17, 2022 (156)
62	HUGCELL_USP	ss5456673453	Oct 17, 2022 (156)
63	1000G_HIGH_COVERAGE	ss5538000772	Oct 17, 2022 (156)
64	SANFORD_IMAGENETICS	ss5634158263	Oct 17, 2022 (156)
65	TOMMO_GENOMICS	ss5697300092	Oct 17, 2022 (156)
66	YY_MCH	ss5804670472	Oct 17, 2022 (156)
67	EVA	ss5843417373	Oct 17, 2022 (156)
68	EVA	ss5854043089	Oct 17, 2022 (156)
69	EVA	ss5861785323	Oct 17, 2022 (156)
70	EVA	ss5962534394	Oct 17, 2022 (156)
71	EVA	ss5980199607	Oct 17, 2022 (156)
72	1000Genomes	NC_000004.11 - 783230	Oct 12, 2018 (152)
73	1000Genomes_30x	NC_000004.12 - 789442	Oct 17, 2022 (156)
74	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 783230	Oct 12, 2018 (152)
75	Genetic variation in the Estonian population	NC_000004.11 - 783230	Oct 12, 2018 (152)
76	The Danish reference pan genome	NC_000004.11 - 783230	Apr 25, 2020 (154)
77	gnomAD - Genomes	NC_000004.12 - 789442	Apr 26, 2021 (155)
78	Genome of the Netherlands Release 5	NC_000004.11 - 783230	Apr 25, 2020 (154)
79	KOREAN population from KRGDB	NC_000004.11 - 783230	Apr 25, 2020 (154)
80	Korean Genome Project	NC_000004.12 - 789442	Apr 25, 2020 (154)
81	Northern Sweden	NC_000004.11 - 783230	Jul 13, 2019 (153)
82	Qatari	NC_000004.11 - 783230	Apr 25, 2020 (154)
83	SGDP_PRJ	NC_000004.11 - 783230	Apr 25, 2020 (154)
84	Siberian	NC_000004.11 - 783230	Apr 25, 2020 (154)
85	8.3KJPN	NC_000004.11 - 783230	Apr 26, 2021 (155)
86	14KJPN	NC_000004.12 - 789442	Oct 17, 2022 (156)
87	TopMed	NC_000004.12 - 789442	Apr 26, 2021 (155)
88	UK 10K study - Twins	NC_000004.11 - 783230	Oct 12, 2018 (152)
89	A Vietnamese Genetic Variation Database	NC_000004.11 - 783230	Jul 13, 2019 (153)
90	ALFA	NC_000004.12 - 789442	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)
rs59422009	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77176318, ss84362008	NC_000004.9:773059:A:C	NC_000004.12:789441:A:C	(self)
ss92436869, ss112842085, ss116835082, ss161886470, ss165986977, ss197886712, ss206332102, ss211342513, ss277536690, ss284828350, ss293052674, ss1589162157	NC_000004.10:773229:A:C	NC_000004.12:789441:A:C	(self)
19394511, 10812183, 7657222, 6542560, 4752612, 11305150, 4056321, 4937140, 10021902, 2643208, 21748314, 10812183, 2364233, ss220689826, ss232222468, ss239551871, ss557249242, ss651001719, ss979665218, ss1071210584, ss1308057521, ss1429737191, ss1580377621, ss1609221398, ss1652215431, ss1800780193, ss1922895210, ss1969636166, ss2022021781, ss2150126854, ss2625511638, ss2705561440, ss2804599039, ss2993979835, ss3345494422, ss3661918974, ss3730771456, ss3761274556, ss3828322402, ss3837592402, ss3858004922, ss3904127756, ss5163779007, ss5346321452, ss5634158263, ss5843417373, ss5962534394, ss5980199607	NC_000004.11:783229:A:C	NC_000004.12:789441:A:C	(self)
25526707, 137687946, 9713671, 31137196, 437303148, 9211306422, ss2259759828, ss3024780547, ss3647631141, ss3711220489, ss3804415588, ss3843025653, ss3953335670, ss4599925592, ss5257713919, ss5456673453, ss5538000772, ss5697300092, ss5804670472, ss5854043089, ss5861785323	NC_000004.12:789441:A:C	NC_000004.12:789441:A:C	(self)
ss10111986, ss16996332	NT_037622.3:773059:A:C	NC_000004.12:789441:A:C	(self)
ss4961207, ss44564485, ss104031647, ss134635180, ss139391251	NT_037622.5:773229:A:C	NC_000004.12:789441: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 rs3775141

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

rs3775141