Name: rs2441752
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.

rs2441752

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:66403598 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.341993 (90522/264690, TOPMED)
C=0.359999 (50392/139978, GnomAD)
C=0.12269 (3467/28258, 14KJPN) (+ 16 more)
C=0.12589 (2110/16760, 8.3KJPN)
T=0.4373 (4362/9974, ALFA)
C=0.2433 (1558/6404, 1000G_30x)
C=0.2416 (1210/5008, 1000G)
T=0.4799 (2150/4480, Estonian)
C=0.4725 (1821/3854, ALSPAC)
C=0.4628 (1716/3708, TWINSUK)
C=0.1314 (385/2930, KOREAN)
C=0.1354 (248/1832, Korea1K)
C=0.425 (424/998, GoNL)
C=0.498 (299/600, NorthernSweden)
C=0.167 (87/520, SGDP_PRJ)
C=0.296 (64/216, Qatari)
C=0.107 (23/214, Vietnamese)
C=0.30 (13/44, Siberian)
T=0.42 (17/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: CTNNA3 : 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	9974	C=0.5627	G=0.0000, T=0.4373
European	Sub	8816	C=0.5802	G=0.0000, T=0.4198
African	Sub	724	C=0.289	G=0.000, T=0.711
African Others	Sub	30	C=0.00	G=0.00, T=1.00
African American	Sub	694	C=0.301	G=0.000, T=0.699
Asian	Sub	4	C=0.2	G=0.0, T=0.8
East Asian	Sub	2	C=0.5	G=0.0, T=0.5
Other Asian	Sub	2	C=0.0	G=0.0, T=1.0
Latin American 1	Sub	22	C=1.00	G=0.00, T=0.00
Latin American 2	Sub	114	C=1.000	G=0.000, T=0.000
South Asian	Sub	8	C=0.5	G=0.0, T=0.5
Other	Sub	286	C=0.514	G=0.000, T=0.486

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=0.341993	T=0.658007
gnomAD - Genomes	Global	Study-wide	139978	C=0.359999	T=0.640001
gnomAD - Genomes	European	Sub	75806	C=0.47136	T=0.52864
gnomAD - Genomes	African	Sub	41946	C=0.16357	T=0.83643
gnomAD - Genomes	American	Sub	13636	C=0.40481	T=0.59519
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.3574	T=0.6426
gnomAD - Genomes	East Asian	Sub	3120	C=0.1147	T=0.8853
gnomAD - Genomes	Other	Sub	2146	C=0.3416	T=0.6584
14KJPN	JAPANESE	Study-wide	28258	C=0.12269	T=0.87731
8.3KJPN	JAPANESE	Study-wide	16760	C=0.12589	T=0.87411
Allele Frequency Aggregator	Total	Global	9974	C=0.5627	G=0.0000, T=0.4373
Allele Frequency Aggregator	European	Sub	8816	C=0.5802	G=0.0000, T=0.4198
Allele Frequency Aggregator	African	Sub	724	C=0.289	G=0.000, T=0.711
Allele Frequency Aggregator	Other	Sub	286	C=0.514	G=0.000, T=0.486
Allele Frequency Aggregator	Latin American 2	Sub	114	C=1.000	G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	22	C=1.00	G=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	8	C=0.5	G=0.0, T=0.5
Allele Frequency Aggregator	Asian	Sub	4	C=0.2	G=0.0, T=0.8
1000Genomes_30x	Global	Study-wide	6404	C=0.2433	T=0.7567
1000Genomes_30x	African	Sub	1786	C=0.1041	T=0.8959
1000Genomes_30x	Europe	Sub	1266	C=0.4889	T=0.5111
1000Genomes_30x	South Asian	Sub	1202	C=0.1697	T=0.8303
1000Genomes_30x	East Asian	Sub	1170	C=0.1068	T=0.8932
1000Genomes_30x	American	Sub	980	C=0.433	T=0.567
1000Genomes	Global	Study-wide	5008	C=0.2416	T=0.7584
1000Genomes	African	Sub	1322	C=0.1059	T=0.8941
1000Genomes	East Asian	Sub	1008	C=0.1111	T=0.8889
1000Genomes	Europe	Sub	1006	C=0.4851	T=0.5149
1000Genomes	South Asian	Sub	978	C=0.177	T=0.823
1000Genomes	American	Sub	694	C=0.428	T=0.572
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.5201	T=0.4799
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.4725	T=0.5275
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.4628	T=0.5372
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.1314	G=0.0000, T=0.8686
Korean Genome Project	KOREAN	Study-wide	1832	C=0.1354	T=0.8646
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.425	T=0.575
Northern Sweden	ACPOP	Study-wide	600	C=0.498	T=0.502
SGDP_PRJ	Global	Study-wide	520	C=0.167	T=0.833
Qatari	Global	Study-wide	216	C=0.296	T=0.704
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.107	T=0.893
Siberian	Global	Study-wide	44	C=0.30	T=0.70
The Danish reference pan genome	Danish	Study-wide	40	C=0.57	T=0.42

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 10	NC_000010.11:g.66403598C>G
GRCh38.p14 chr 10	NC_000010.11:g.66403598C>T
GRCh37.p13 chr 10	NC_000010.10:g.68163356C>G
GRCh37.p13 chr 10	NC_000010.10:g.68163356C>T
CTNNA3 RefSeqGene	NG_034072.1:g.1297594G>C
CTNNA3 RefSeqGene	NG_034072.1:g.1297594G>A

Gene: CTNNA3, catenin alpha 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
CTNNA3 transcript variant 2	NM_001127384.3:c.1532-242… NM_001127384.3:c.1532-24246G>C	N/A	Intron Variant
CTNNA3 transcript variant 1	NM_013266.4:c.1532-24246G… NM_013266.4:c.1532-24246G>C	N/A	Intron Variant
CTNNA3 transcript variant 3	NM_001291133.2:c.	N/A	Genic Downstream Transcript Variant
CTNNA3 transcript variant X1	XM_017016151.2:c.1601-242… XM_017016151.2:c.1601-24246G>C	N/A	Intron Variant
CTNNA3 transcript variant X2	XM_017016152.2:c.1757-242… XM_017016152.2:c.1757-24246G>C	N/A	Intron Variant
CTNNA3 transcript variant X5	XM_017016155.3:c.749-2424… XM_017016155.3:c.749-24246G>C	N/A	Intron Variant
CTNNA3 transcript variant X4	XM_017016156.2:c.749-2424… XM_017016156.2:c.749-24246G>C	N/A	Intron Variant
CTNNA3 transcript variant X6	XM_017016157.3:c.437-2424… XM_017016157.3:c.437-24246G>C	N/A	Intron Variant
CTNNA3 transcript variant X3	XM_047425124.1:c.1568-242… XM_047425124.1:c.1568-24246G>C	N/A	Intron Variant
CTNNA3 transcript variant X7	XM_017016158.3:c.	N/A	Genic Downstream 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=	G	T
GRCh38.p14 chr 10	NC_000010.11:g.66403598=	NC_000010.11:g.66403598C>G	NC_000010.11:g.66403598C>T
GRCh37.p13 chr 10	NC_000010.10:g.68163356=	NC_000010.10:g.68163356C>G	NC_000010.10:g.68163356C>T
CTNNA3 RefSeqGene	NG_034072.1:g.1297594=	NG_034072.1:g.1297594G>C	NG_034072.1:g.1297594G>A
CTNNA3 transcript variant 2	NM_001127384.1:c.1532-24246=	NM_001127384.1:c.1532-24246G>C	NM_001127384.1:c.1532-24246G>A
CTNNA3 transcript variant 2	NM_001127384.3:c.1532-24246=	NM_001127384.3:c.1532-24246G>C	NM_001127384.3:c.1532-24246G>A
CTNNA3 transcript variant 1	NM_013266.2:c.1532-24246=	NM_013266.2:c.1532-24246G>C	NM_013266.2:c.1532-24246G>A
CTNNA3 transcript variant 1	NM_013266.4:c.1532-24246=	NM_013266.4:c.1532-24246G>C	NM_013266.4:c.1532-24246G>A
CTNNA3 transcript variant X1	XM_005269717.1:c.1568-24246=	XM_005269717.1:c.1568-24246G>C	XM_005269717.1:c.1568-24246G>A
CTNNA3 transcript variant X1	XM_017016151.2:c.1601-24246=	XM_017016151.2:c.1601-24246G>C	XM_017016151.2:c.1601-24246G>A
CTNNA3 transcript variant X2	XM_017016152.2:c.1757-24246=	XM_017016152.2:c.1757-24246G>C	XM_017016152.2:c.1757-24246G>A
CTNNA3 transcript variant X5	XM_017016155.3:c.749-24246=	XM_017016155.3:c.749-24246G>C	XM_017016155.3:c.749-24246G>A
CTNNA3 transcript variant X4	XM_017016156.2:c.749-24246=	XM_017016156.2:c.749-24246G>C	XM_017016156.2:c.749-24246G>A
CTNNA3 transcript variant X6	XM_017016157.3:c.437-24246=	XM_017016157.3:c.437-24246G>C	XM_017016157.3:c.437-24246G>A
CTNNA3 transcript variant X3	XM_047425124.1:c.1568-24246=	XM_047425124.1:c.1568-24246G>C	XM_047425124.1:c.1568-24246G>A

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#.

74 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss3422726	Sep 28, 2001 (100)
2	SC_JCM	ss4121495	Nov 05, 2001 (101)
3	TSC-CSHL	ss5551515	Oct 08, 2002 (108)
4	SC_SNP	ss12957583	Dec 05, 2003 (130)
5	SC_SNP	ss15562338	Feb 27, 2004 (120)
6	SSAHASNP	ss20667030	Apr 05, 2004 (123)
7	ABI	ss39740356	Mar 15, 2006 (126)
8	HGSV	ss79688329	Dec 14, 2007 (130)
9	HGSV	ss85140746	Dec 14, 2007 (130)
10	BCMHGSC_JDW	ss88250913	Mar 23, 2008 (129)
11	BGI	ss106683772	Feb 04, 2009 (130)
12	1000GENOMES	ss109524729	Jan 24, 2009 (130)
13	1000GENOMES	ss113401317	Jan 25, 2009 (130)
14	ILLUMINA-UK	ss119205427	Dec 01, 2009 (131)
15	ENSEMBL	ss131924801	Dec 01, 2009 (131)
16	ENSEMBL	ss142768318	Dec 01, 2009 (131)
17	GMI	ss155166385	Dec 01, 2009 (131)
18	COMPLETE_GENOMICS	ss170283615	Jul 04, 2010 (132)
19	BUSHMAN	ss201643762	Jul 04, 2010 (132)
20	1000GENOMES	ss224780275	Jul 14, 2010 (132)
21	1000GENOMES	ss235216230	Jul 15, 2010 (132)
22	1000GENOMES	ss241914113	Jul 15, 2010 (132)
23	GMI	ss280657140	May 04, 2012 (137)
24	PJP	ss290859563	May 09, 2011 (134)
25	TISHKOFF	ss562017566	Apr 25, 2013 (138)
26	SSMP	ss656885048	Apr 25, 2013 (138)
27	EVA-GONL	ss987592941	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1077065319	Aug 21, 2014 (142)
29	1000GENOMES	ss1337828455	Aug 21, 2014 (142)
30	DDI	ss1426352416	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1575179925	Apr 01, 2015 (144)
32	EVA_DECODE	ss1597262580	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1624772651	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1667766684	Apr 01, 2015 (144)
35	HAMMER_LAB	ss1806434215	Sep 08, 2015 (146)
36	WEILL_CORNELL_DGM	ss1930956335	Feb 12, 2016 (147)
37	GENOMED	ss1967153638	Jul 19, 2016 (147)
38	JJLAB	ss2026203677	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2154476551	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2175551572	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2627571656	Nov 08, 2017 (151)
42	GRF	ss2698721511	Nov 08, 2017 (151)
43	GNOMAD	ss2889878183	Nov 08, 2017 (151)
44	SWEGEN	ss3006638224	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3026893186	Nov 08, 2017 (151)
46	CSHL	ss3349169390	Nov 08, 2017 (151)
47	URBANLAB	ss3649396047	Oct 12, 2018 (152)
48	EGCUT_WGS	ss3674053999	Jul 13, 2019 (153)
49	EVA_DECODE	ss3690071564	Jul 13, 2019 (153)
50	ACPOP	ss3737409373	Jul 13, 2019 (153)
51	EVA	ss3748220840	Jul 13, 2019 (153)
52	PACBIO	ss3786700919	Jul 13, 2019 (153)
53	PACBIO	ss3791877813	Jul 13, 2019 (153)
54	PACBIO	ss3796759836	Jul 13, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3813595955	Jul 13, 2019 (153)
56	EVA	ss3832175726	Apr 26, 2020 (154)
57	EVA	ss3839627721	Apr 26, 2020 (154)
58	EVA	ss3845100211	Apr 26, 2020 (154)
59	SGDP_PRJ	ss3874410906	Apr 26, 2020 (154)
60	KRGDB	ss3922490014	Apr 26, 2020 (154)
61	KOGIC	ss3968065201	Apr 26, 2020 (154)
62	TOPMED	ss4855797802	Apr 27, 2021 (155)
63	TOMMO_GENOMICS	ss5198067245	Apr 27, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5284389248	Oct 16, 2022 (156)
65	EVA	ss5394072654	Oct 16, 2022 (156)
66	HUGCELL_USP	ss5479933441	Oct 16, 2022 (156)
67	1000G_HIGH_COVERAGE	ss5578512865	Oct 16, 2022 (156)
68	SANFORD_IMAGENETICS	ss5649484708	Oct 16, 2022 (156)
69	TOMMO_GENOMICS	ss5744021195	Oct 16, 2022 (156)
70	YY_MCH	ss5811617351	Oct 16, 2022 (156)
71	EVA	ss5824532211	Oct 16, 2022 (156)
72	EVA	ss5849609375	Oct 16, 2022 (156)
73	EVA	ss5879294202	Oct 16, 2022 (156)
74	EVA	ss5940759131	Oct 16, 2022 (156)
75	1000Genomes	NC_000010.10 - 68163356	Oct 12, 2018 (152)
76	1000Genomes_30x	NC_000010.11 - 66403598	Oct 16, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 68163356	Oct 12, 2018 (152)
78	Genetic variation in the Estonian population	NC_000010.10 - 68163356	Oct 12, 2018 (152)
79	The Danish reference pan genome	NC_000010.10 - 68163356	Apr 26, 2020 (154)
80	gnomAD - Genomes	NC_000010.11 - 66403598	Apr 27, 2021 (155)
81	Genome of the Netherlands Release 5	NC_000010.10 - 68163356	Apr 26, 2020 (154)
82	KOREAN population from KRGDB	NC_000010.10 - 68163356	Apr 26, 2020 (154)
83	Korean Genome Project	NC_000010.11 - 66403598	Apr 26, 2020 (154)
84	Northern Sweden	NC_000010.10 - 68163356	Jul 13, 2019 (153)
85	Qatari	NC_000010.10 - 68163356	Apr 26, 2020 (154)
86	SGDP_PRJ	NC_000010.10 - 68163356	Apr 26, 2020 (154)
87	Siberian	NC_000010.10 - 68163356	Apr 26, 2020 (154)
88	8.3KJPN	NC_000010.10 - 68163356	Apr 27, 2021 (155)
89	14KJPN	NC_000010.11 - 66403598	Oct 16, 2022 (156)
90	TopMed	NC_000010.11 - 66403598	Apr 27, 2021 (155)
91	UK 10K study - Twins	NC_000010.10 - 68163356	Oct 12, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000010.10 - 68163356	Jul 13, 2019 (153)
93	ALFA	NC_000010.11 - 66403598	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).

Associated ID	History Updated (Build)
rs9415847	May 23, 2008 (130)
rs12771475	Sep 24, 2004 (123)
rs57053191	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
29667408, ss3922490014	NC_000010.10:68163355:C:G	NC_000010.11:66403597:C:G	(self)
9885576757	NC_000010.11:66403597:C:G	NC_000010.11:66403597:C:G	(self)
ss79688329, ss85140746	NC_000010.8:67833361:C:T	NC_000010.11:66403597:C:T	(self)
ss88250913, ss109524729, ss113401317, ss119205427, ss170283615, ss201643762, ss280657140, ss290859563, ss1597262580	NC_000010.9:67833361:C:T	NC_000010.11:66403597:C:T	(self)
50230841, 27880364, 19792247, 2199730, 12434311, 29667408, 10694238, 12998265, 26427886, 6992905, 56036552, 27880364, 6193505, ss224780275, ss235216230, ss241914113, ss562017566, ss656885048, ss987592941, ss1077065319, ss1337828455, ss1426352416, ss1575179925, ss1624772651, ss1667766684, ss1806434215, ss1930956335, ss1967153638, ss2026203677, ss2154476551, ss2627571656, ss2698721511, ss2889878183, ss3006638224, ss3349169390, ss3674053999, ss3737409373, ss3748220840, ss3786700919, ss3791877813, ss3796759836, ss3832175726, ss3839627721, ss3874410906, ss3922490014, ss5198067245, ss5394072654, ss5649484708, ss5824532211, ss5940759131	NC_000010.10:68163355:C:T	NC_000010.11:66403597:C:T	(self)
66038800, 355022321, 24443202, 77858299, 71343457, 9885576757, ss2175551572, ss3026893186, ss3649396047, ss3690071564, ss3813595955, ss3845100211, ss3968065201, ss4855797802, ss5284389248, ss5479933441, ss5578512865, ss5744021195, ss5811617351, ss5849609375, ss5879294202	NC_000010.11:66403597:C:T	NC_000010.11:66403597:C:T	(self)
ss12957583	NT_008583.15:16714503:C:T	NC_000010.11:66403597:C:T	(self)
ss15562338, ss20667030	NT_008583.16:16714510:C:T	NC_000010.11:66403597:C:T	(self)
ss3422726, ss4121495, ss5551515, ss39740356, ss106683772, ss131924801, ss142768318, ss155166385	NT_030059.13:18967819:C:T	NC_000010.11:66403597:C:T	(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 rs2441752

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

rs2441752