Name: rs12807920
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.

rs12807920

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr11:99620806 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.457819 (121180/264690, TOPMED)
T=0.447067 (62457/139704, GnomAD)
C=0.46716 (13201/28258, 14KJPN) (+ 17 more)
T=0.48206 (12384/25690, ALFA)
C=0.46802 (7843/16758, 8.3KJPN)
T=0.4636 (2969/6404, 1000G_30x)
T=0.4669 (2338/5008, 1000G)
T=0.4895 (2193/4480, Estonian)
T=0.4655 (1794/3854, ALSPAC)
T=0.4957 (1838/3708, TWINSUK)
C=0.4618 (1353/2930, KOREAN)
T=0.4635 (877/1892, HapMap)
C=0.4596 (842/1832, Korea1K)
T=0.486 (485/998, GoNL)
T=0.497 (298/600, NorthernSweden)
C=0.302 (139/460, SGDP_PRJ)
C=0.472 (102/216, Qatari)
T=0.381 (80/210, Vietnamese)
T=0.25 (10/40, GENOME_DK)
C=0.44 (14/32, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CNTN5 : Intron Variant
Publications: 2 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	25690	C=0.51794	T=0.48206
European	Sub	17392	C=0.51719	T=0.48281
African	Sub	3622	C=0.6549	T=0.3451
African Others	Sub	126	C=0.690	T=0.310
African American	Sub	3496	C=0.6536	T=0.3464
Asian	Sub	160	C=0.494	T=0.506
East Asian	Sub	102	C=0.539	T=0.461
Other Asian	Sub	58	C=0.41	T=0.59
Latin American 1	Sub	290	C=0.500	T=0.500
Latin American 2	Sub	2770	C=0.3635	T=0.6365
South Asian	Sub	110	C=0.464	T=0.536
Other	Sub	1346	C=0.4881	T=0.5119

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	C=0.542181	T=0.457819
gnomAD - Genomes	Global	Study-wide	139704	C=0.552933	T=0.447067
gnomAD - Genomes	European	Sub	75642	C=0.52555	T=0.47445
gnomAD - Genomes	African	Sub	41856	C=0.66074	T=0.33926
gnomAD - Genomes	American	Sub	13612	C=0.40714	T=0.59286
gnomAD - Genomes	Ashkenazi Jewish	Sub	3316	C=0.4976	T=0.5024
gnomAD - Genomes	East Asian	Sub	3126	C=0.4747	T=0.5253
gnomAD - Genomes	Other	Sub	2152	C=0.5395	T=0.4605
14KJPN	JAPANESE	Study-wide	28258	C=0.46716	T=0.53284
Allele Frequency Aggregator	Total	Global	25690	C=0.51794	T=0.48206
Allele Frequency Aggregator	European	Sub	17392	C=0.51719	T=0.48281
Allele Frequency Aggregator	African	Sub	3622	C=0.6549	T=0.3451
Allele Frequency Aggregator	Latin American 2	Sub	2770	C=0.3635	T=0.6365
Allele Frequency Aggregator	Other	Sub	1346	C=0.4881	T=0.5119
Allele Frequency Aggregator	Latin American 1	Sub	290	C=0.500	T=0.500
Allele Frequency Aggregator	Asian	Sub	160	C=0.494	T=0.506
Allele Frequency Aggregator	South Asian	Sub	110	C=0.464	T=0.536
8.3KJPN	JAPANESE	Study-wide	16758	C=0.46802	T=0.53198
1000Genomes_30x	Global	Study-wide	6404	C=0.5364	T=0.4636
1000Genomes_30x	African	Sub	1786	C=0.6590	T=0.3410
1000Genomes_30x	Europe	Sub	1266	C=0.5253	T=0.4747
1000Genomes_30x	South Asian	Sub	1202	C=0.5641	T=0.4359
1000Genomes_30x	East Asian	Sub	1170	C=0.4718	T=0.5282
1000Genomes_30x	American	Sub	980	C=0.370	T=0.630
1000Genomes	Global	Study-wide	5008	C=0.5331	T=0.4669
1000Genomes	African	Sub	1322	C=0.6536	T=0.3464
1000Genomes	East Asian	Sub	1008	C=0.4663	T=0.5337
1000Genomes	Europe	Sub	1006	C=0.5268	T=0.4732
1000Genomes	South Asian	Sub	978	C=0.562	T=0.438
1000Genomes	American	Sub	694	C=0.369	T=0.631
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.5105	T=0.4895
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.5345	T=0.4655
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.5043	T=0.4957
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.4618	T=0.5382
HapMap	Global	Study-wide	1892	C=0.5365	T=0.4635
HapMap	American	Sub	770	C=0.518	T=0.482
HapMap	African	Sub	692	C=0.595	T=0.405
HapMap	Asian	Sub	254	C=0.457	T=0.543
HapMap	Europe	Sub	176	C=0.500	T=0.500
Korean Genome Project	KOREAN	Study-wide	1832	C=0.4596	T=0.5404
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.514	T=0.486
Northern Sweden	ACPOP	Study-wide	600	C=0.503	T=0.497
SGDP_PRJ	Global	Study-wide	460	C=0.302	T=0.698
Qatari	Global	Study-wide	216	C=0.472	T=0.528
A Vietnamese Genetic Variation Database	Global	Study-wide	210	C=0.619	T=0.381
The Danish reference pan genome	Danish	Study-wide	40	C=0.75	T=0.25
Siberian	Global	Study-wide	32	C=0.44	T=0.56

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 11	NC_000011.10:g.99620806C>T
GRCh37.p13 chr 11	NC_000011.9:g.99491537C>T
CNTN5 RefSeqGene	NG_047156.1:g.604831C>T

Gene: CNTN5, contactin 5 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CNTN5 transcript variant 2	NM_001243270.2:c.55+64537… NM_001243270.2:c.55+64537C>T	N/A	Intron Variant
CNTN5 transcript variant 4	NM_001243271.2:c.55+64537… NM_001243271.2:c.55+64537C>T	N/A	Intron Variant
CNTN5 transcript variant 1	NM_014361.4:c.55+64537C>T	N/A	Intron Variant
CNTN5 transcript variant 3	NM_175566.2:c.55+64537C>T	N/A	Intron Variant
CNTN5 transcript variant X2	XM_011542871.2:c.55+64537… XM_011542871.2:c.55+64537C>T	N/A	Intron Variant
CNTN5 transcript variant X4	XM_011542873.2:c.55+64537… XM_011542873.2:c.55+64537C>T	N/A	Intron Variant
CNTN5 transcript variant X1	XM_017017926.2:c.55+64537… XM_017017926.2:c.55+64537C>T	N/A	Intron Variant
CNTN5 transcript variant X5	XM_017017927.2:c.55+64537… XM_017017927.2:c.55+64537C>T	N/A	Intron Variant
CNTN5 transcript variant X6	XM_017017928.2:c.55+64537… XM_017017928.2:c.55+64537C>T	N/A	Intron Variant
CNTN5 transcript variant X8	XM_017017929.2:c.55+64537… XM_017017929.2:c.55+64537C>T	N/A	Intron Variant
CNTN5 transcript variant X3	XM_047427130.1:c.55+64537… XM_047427130.1:c.55+64537C>T	N/A	Intron Variant
CNTN5 transcript variant X7	XM_047427131.1:c.55+64537… XM_047427131.1:c.55+64537C>T	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	C=	T
GRCh38.p14 chr 11	NC_000011.10:g.99620806=	NC_000011.10:g.99620806C>T
GRCh37.p13 chr 11	NC_000011.9:g.99491537=	NC_000011.9:g.99491537C>T
CNTN5 RefSeqGene	NG_047156.1:g.604831=	NG_047156.1:g.604831C>T
CNTN5 transcript variant 2	NM_001243270.1:c.55+64537=	NM_001243270.1:c.55+64537C>T
CNTN5 transcript variant 2	NM_001243270.2:c.55+64537=	NM_001243270.2:c.55+64537C>T
CNTN5 transcript variant 4	NM_001243271.1:c.55+64537=	NM_001243271.1:c.55+64537C>T
CNTN5 transcript variant 4	NM_001243271.2:c.55+64537=	NM_001243271.2:c.55+64537C>T
CNTN5 transcript variant 1	NM_014361.3:c.55+64537=	NM_014361.3:c.55+64537C>T
CNTN5 transcript variant 1	NM_014361.4:c.55+64537=	NM_014361.4:c.55+64537C>T
CNTN5 transcript variant 3	NM_175566.2:c.55+64537=	NM_175566.2:c.55+64537C>T
CNTN5 transcript variant X2	XM_011542871.2:c.55+64537=	XM_011542871.2:c.55+64537C>T
CNTN5 transcript variant X4	XM_011542873.2:c.55+64537=	XM_011542873.2:c.55+64537C>T
CNTN5 transcript variant X1	XM_017017926.2:c.55+64537=	XM_017017926.2:c.55+64537C>T
CNTN5 transcript variant X5	XM_017017927.2:c.55+64537=	XM_017017927.2:c.55+64537C>T
CNTN5 transcript variant X6	XM_017017928.2:c.55+64537=	XM_017017928.2:c.55+64537C>T
CNTN5 transcript variant X8	XM_017017929.2:c.55+64537=	XM_017017929.2:c.55+64537C>T
CNTN5 transcript variant X3	XM_047427130.1:c.55+64537=	XM_047427130.1:c.55+64537C>T
CNTN5 transcript variant X7	XM_047427131.1:c.55+64537=	XM_047427131.1:c.55+64537C>T

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#.

70 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss20857099	Apr 05, 2004 (121)
2	PERLEGEN	ss24576989	Sep 20, 2004 (123)
3	AFFY	ss66421111	Dec 01, 2006 (127)
4	PERLEGEN	ss69326254	May 17, 2007 (127)
5	AFFY	ss76186676	Dec 07, 2007 (129)
6	KRIBB_YJKIM	ss83018627	Dec 17, 2007 (130)
7	BCMHGSC_JDW	ss88733609	Mar 24, 2008 (129)
8	BGI	ss102992447	Dec 01, 2009 (131)
9	1000GENOMES	ss110934402	Jan 25, 2009 (130)
10	1000GENOMES	ss115049192	Jan 25, 2009 (130)
11	ENSEMBL	ss132050888	Dec 01, 2009 (131)
12	ENSEMBL	ss132766524	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss170726888	Jul 04, 2010 (132)
14	AFFY	ss172746140	Jul 04, 2010 (132)
15	BUSHMAN	ss203106542	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss207743298	Jul 04, 2010 (132)
17	1000GENOMES	ss225416876	Jul 14, 2010 (132)
18	1000GENOMES	ss235685318	Jul 15, 2010 (132)
19	1000GENOMES	ss242290627	Jul 15, 2010 (132)
20	BL	ss255354186	May 09, 2011 (134)
21	GMI	ss281138422	May 04, 2012 (137)
22	GMI	ss286440585	Apr 25, 2013 (138)
23	PJP	ss291121479	May 09, 2011 (134)
24	TISHKOFF	ss562772608	Apr 25, 2013 (138)
25	SSMP	ss658293342	Apr 25, 2013 (138)
26	EVA-GONL	ss988873875	Aug 21, 2014 (142)
27	JMKIDD_LAB	ss1077979640	Aug 21, 2014 (142)
28	1000GENOMES	ss1342631092	Aug 21, 2014 (142)
29	DDI	ss1426734504	Apr 01, 2015 (144)
30	EVA_GENOME_DK	ss1575900135	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1627283162	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1670277195	Apr 01, 2015 (144)
33	EVA_SVP	ss1713278336	Apr 01, 2015 (144)
34	HAMMER_LAB	ss1806959557	Sep 08, 2015 (146)
35	WEILL_CORNELL_DGM	ss1932237015	Feb 12, 2016 (147)
36	GENOMED	ss1967436737	Jul 19, 2016 (147)
37	JJLAB	ss2026861532	Sep 14, 2016 (149)
38	USC_VALOUEV	ss2155173722	Dec 20, 2016 (150)
39	HUMAN_LONGEVITY	ss2185010525	Dec 20, 2016 (150)
40	SYSTEMSBIOZJU	ss2627903936	Nov 08, 2017 (151)
41	GRF	ss2699477233	Nov 08, 2017 (151)
42	GNOMAD	ss2903510349	Nov 08, 2017 (151)
43	SWEGEN	ss3008645703	Nov 08, 2017 (151)
44	BIOINF_KMB_FNS_UNIBA	ss3027228773	Nov 08, 2017 (151)
45	CSHL	ss3349754918	Nov 08, 2017 (151)
46	URBANLAB	ss3649685079	Oct 12, 2018 (152)
47	EGCUT_WGS	ss3675965565	Jul 13, 2019 (153)
48	EVA_DECODE	ss3692438687	Jul 13, 2019 (153)
49	ACPOP	ss3738467597	Jul 13, 2019 (153)
50	EVA	ss3749708690	Jul 13, 2019 (153)
51	KHV_HUMAN_GENOMES	ss3815041954	Jul 13, 2019 (153)
52	EVA	ss3832796288	Apr 26, 2020 (154)
53	EVA	ss3839958785	Apr 26, 2020 (154)
54	EVA	ss3845439853	Apr 26, 2020 (154)
55	SGDP_PRJ	ss3876966134	Apr 26, 2020 (154)
56	KRGDB	ss3925403640	Apr 26, 2020 (154)
57	KOGIC	ss3970589197	Apr 26, 2020 (154)
58	TOPMED	ss4897026125	Apr 26, 2021 (155)
59	TOMMO_GENOMICS	ss5203519152	Apr 26, 2021 (155)
60	1000G_HIGH_COVERAGE	ss5288611924	Oct 16, 2022 (156)
61	HUGCELL_USP	ss5483631393	Oct 16, 2022 (156)
62	EVA	ss5510487069	Oct 16, 2022 (156)
63	1000G_HIGH_COVERAGE	ss5584945379	Oct 16, 2022 (156)
64	SANFORD_IMAGENETICS	ss5651905889	Oct 16, 2022 (156)
65	TOMMO_GENOMICS	ss5751861829	Oct 16, 2022 (156)
66	YY_MCH	ss5812705938	Oct 16, 2022 (156)
67	EVA	ss5837114553	Oct 16, 2022 (156)
68	EVA	ss5850114458	Oct 16, 2022 (156)
69	EVA	ss5921320334	Oct 16, 2022 (156)
70	EVA	ss5943226940	Oct 16, 2022 (156)
71	1000Genomes	NC_000011.9 - 99491537	Oct 12, 2018 (152)
72	1000Genomes_30x	NC_000011.10 - 99620806	Oct 16, 2022 (156)
73	The Avon Longitudinal Study of Parents and Children	NC_000011.9 - 99491537	Oct 12, 2018 (152)
74	Genetic variation in the Estonian population	NC_000011.9 - 99491537	Oct 12, 2018 (152)
75	The Danish reference pan genome	NC_000011.9 - 99491537	Apr 26, 2020 (154)
76	gnomAD - Genomes	NC_000011.10 - 99620806	Apr 26, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000011.9 - 99491537	Apr 26, 2020 (154)
78	HapMap	NC_000011.10 - 99620806	Apr 26, 2020 (154)
79	KOREAN population from KRGDB	NC_000011.9 - 99491537	Apr 26, 2020 (154)
80	Korean Genome Project	NC_000011.10 - 99620806	Apr 26, 2020 (154)
81	Northern Sweden	NC_000011.9 - 99491537	Jul 13, 2019 (153)
82	Qatari	NC_000011.9 - 99491537	Apr 26, 2020 (154)
83	SGDP_PRJ	NC_000011.9 - 99491537	Apr 26, 2020 (154)
84	Siberian	NC_000011.9 - 99491537	Apr 26, 2020 (154)
85	8.3KJPN	NC_000011.9 - 99491537	Apr 26, 2021 (155)
86	14KJPN	NC_000011.10 - 99620806	Oct 16, 2022 (156)
87	TopMed	NC_000011.10 - 99620806	Apr 26, 2021 (155)
88	UK 10K study - Twins	NC_000011.9 - 99491537	Oct 12, 2018 (152)
89	A Vietnamese Genetic Variation Database	NC_000011.9 - 99491537	Jul 13, 2019 (153)
90	ALFA	NC_000011.10 - 99620806	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)
rs17604215	Oct 08, 2004 (123)
rs61716117	Feb 26, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss88733609, ss110934402, ss115049192, ss170726888, ss203106542, ss207743298, ss255354186, ss281138422, ss286440585, ss291121479, ss1713278336	NC_000011.8:98996746:C:T	NC_000011.10:99620805:C:T	(self)
55200570, 30634602, 21703813, 2700057, 13672716, 32581034, 11752462, 14278945, 28983114, 7690076, 61488459, 30634602, 6798103, ss225416876, ss235685318, ss242290627, ss562772608, ss658293342, ss988873875, ss1077979640, ss1342631092, ss1426734504, ss1575900135, ss1627283162, ss1670277195, ss1806959557, ss1932237015, ss1967436737, ss2026861532, ss2155173722, ss2627903936, ss2699477233, ss2903510349, ss3008645703, ss3349754918, ss3675965565, ss3738467597, ss3749708690, ss3832796288, ss3839958785, ss3876966134, ss3925403640, ss5203519152, ss5510487069, ss5651905889, ss5837114553, ss5943226940	NC_000011.9:99491536:C:T	NC_000011.10:99620805:C:T	(self)
72471314, 389541703, 678964, 26967198, 85698933, 112571781, 9762696683, ss2185010525, ss3027228773, ss3649685079, ss3692438687, ss3815041954, ss3845439853, ss3970589197, ss4897026125, ss5288611924, ss5483631393, ss5584945379, ss5751861829, ss5812705938, ss5850114458, ss5921320334	NC_000011.10:99620805:C:T	NC_000011.10:99620805:C:T	(self)
ss20857099	NT_033899.6:3035388:C:T	NC_000011.10:99620805:C:T	(self)
ss24576989, ss66421111, ss69326254, ss76186676, ss83018627, ss102992447, ss132050888, ss132766524, ss172746140	NT_033899.8:3053952:C:T	NC_000011.10:99620805:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

2 citations for rs12807920

PMID	Title	Author	Year	Journal
19169254	Genome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways.	Nair RP et al.	2009	Nature genetics
21424828	The efficacy of detecting variants with small effects on the Affymetrix 6.0 platform using pooled DNA.	Chiang CW et al.	2011	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

rs12807920