Name: rs11187996
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.

rs11187996

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr10:94515272 (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 / A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.447165 (118360/264690, TOPMED)
C=0.440304 (61425/139506, GnomAD)
A=0.35855 (10129/28250, 14KJPN) (+ 15 more)
C=0.43849 (8283/18890, ALFA)
A=0.35931 (6022/16760, 8.3KJPN)
A=0.4900 (3138/6404, 1000G_30x)
A=0.4792 (2400/5008, 1000G)
C=0.4158 (1863/4480, Estonian)
C=0.4468 (1722/3854, ALSPAC)
C=0.4412 (1636/3708, TWINSUK)
A=0.2812 (824/2930, KOREAN)
A=0.2669 (489/1832, Korea1K)
C=0.449 (448/998, GoNL)
C=0.435 (261/600, NorthernSweden)
A=0.307 (124/404, SGDP_PRJ)
C=0.375 (81/216, Qatari)
A=0.41 (18/44, Siberian)
C=0.35 (14/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TBC1D12 : 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=0.56151	C=0.43849
European	Sub	14286	A=0.56755	C=0.43245
African	Sub	2946	A=0.5377	C=0.4623
African Others	Sub	114	A=0.509	C=0.491
African American	Sub	2832	A=0.5388	C=0.4612
Asian	Sub	112	A=0.375	C=0.625
East Asian	Sub	86	A=0.36	C=0.64
Other Asian	Sub	26	A=0.42	C=0.58
Latin American 1	Sub	146	A=0.562	C=0.438
Latin American 2	Sub	610	A=0.648	C=0.352
South Asian	Sub	98	A=0.33	C=0.67
Other	Sub	692	A=0.526	C=0.474

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=0.552835	C=0.447165
gnomAD - Genomes	Global	Study-wide	139506	A=0.559696	C=0.440304
gnomAD - Genomes	European	Sub	75608	A=0.57157	C=0.42843
gnomAD - Genomes	African	Sub	41742	A=0.53855	C=0.46145
gnomAD - Genomes	American	Sub	13584	A=0.61911	C=0.38089
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	A=0.5942	C=0.4058
gnomAD - Genomes	East Asian	Sub	3114	A=0.2617	C=0.7383
gnomAD - Genomes	Other	Sub	2136	A=0.5557	C=0.4443
14KJPN	JAPANESE	Study-wide	28250	A=0.35855	C=0.64145
Allele Frequency Aggregator	Total	Global	18890	A=0.56151	C=0.43849
Allele Frequency Aggregator	European	Sub	14286	A=0.56755	C=0.43245
Allele Frequency Aggregator	African	Sub	2946	A=0.5377	C=0.4623
Allele Frequency Aggregator	Other	Sub	692	A=0.526	C=0.474
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.648	C=0.352
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.562	C=0.438
Allele Frequency Aggregator	Asian	Sub	112	A=0.375	C=0.625
Allele Frequency Aggregator	South Asian	Sub	98	A=0.33	C=0.67
8.3KJPN	JAPANESE	Study-wide	16760	A=0.35931	C=0.64069
1000Genomes_30x	Global	Study-wide	6404	A=0.4900	C=0.5100
1000Genomes_30x	African	Sub	1786	A=0.5644	C=0.4356
1000Genomes_30x	Europe	Sub	1266	A=0.5608	C=0.4392
1000Genomes_30x	South Asian	Sub	1202	A=0.4143	C=0.5857
1000Genomes_30x	East Asian	Sub	1170	A=0.2359	C=0.7641
1000Genomes_30x	American	Sub	980	A=0.659	C=0.341
1000Genomes	Global	Study-wide	5008	A=0.4792	C=0.5208
1000Genomes	African	Sub	1322	A=0.5582	C=0.4418
1000Genomes	East Asian	Sub	1008	A=0.2411	C=0.7589
1000Genomes	Europe	Sub	1006	A=0.5567	C=0.4433
1000Genomes	South Asian	Sub	978	A=0.400	C=0.600
1000Genomes	American	Sub	694	A=0.674	C=0.326
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.5842	C=0.4158
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.5532	C=0.4468
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.5588	C=0.4412
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.2812	C=0.7188, G=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	A=0.2669	C=0.7331
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.551	C=0.449
Northern Sweden	ACPOP	Study-wide	600	A=0.565	C=0.435
SGDP_PRJ	Global	Study-wide	404	A=0.307	C=0.693
Qatari	Global	Study-wide	216	A=0.625	C=0.375
Siberian	Global	Study-wide	44	A=0.41	C=0.59
The Danish reference pan genome	Danish	Study-wide	40	A=0.65	C=0.35

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.94515272A>C
GRCh38.p14 chr 10	NC_000010.11:g.94515272A>G
GRCh37.p13 chr 10	NC_000010.10:g.96275029A>C
GRCh37.p13 chr 10	NC_000010.10:g.96275029A>G

Gene: TBC1D12, TBC1 domain family member 12 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TBC1D12 transcript	NM_015188.2:c.1761+3618A>C	N/A	Intron Variant
TBC1D12 transcript variant X1	XM_006717732.5:c.1680+361… XM_006717732.5:c.1680+3618A>C	N/A	Intron Variant
TBC1D12 transcript variant X5	XM_011539558.4:c.855+3618… XM_011539558.4:c.855+3618A>C	N/A	Intron Variant
TBC1D12 transcript variant X6	XM_017015998.3:c.492+3618… XM_017015998.3:c.492+3618A>C	N/A	Intron Variant
TBC1D12 transcript variant X8	XM_017015999.3:c.492+3618… XM_017015999.3:c.492+3618A>C	N/A	Intron Variant
TBC1D12 transcript variant X2	XM_047424905.1:c.1761+361… XM_047424905.1:c.1761+3618A>C	N/A	Intron Variant
TBC1D12 transcript variant X7	XM_047424907.1:c.492+3618… XM_047424907.1:c.492+3618A>C	N/A	Intron Variant
TBC1D12 transcript variant X3	XM_047424906.1:c.	N/A	Genic Downstream Transcript Variant
TBC1D12 transcript variant X4	XR_945637.3:n.	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	A=	C	G
GRCh38.p14 chr 10	NC_000010.11:g.94515272=	NC_000010.11:g.94515272A>C	NC_000010.11:g.94515272A>G
GRCh37.p13 chr 10	NC_000010.10:g.96275029=	NC_000010.10:g.96275029A>C	NC_000010.10:g.96275029A>G
TBC1D12 transcript	NM_015188.1:c.1761+3618=	NM_015188.1:c.1761+3618A>C	NM_015188.1:c.1761+3618A>G
TBC1D12 transcript	NM_015188.2:c.1761+3618=	NM_015188.2:c.1761+3618A>C	NM_015188.2:c.1761+3618A>G
TBC1D12 transcript variant X1	XM_006717732.5:c.1680+3618=	XM_006717732.5:c.1680+3618A>C	XM_006717732.5:c.1680+3618A>G
TBC1D12 transcript variant X5	XM_011539558.4:c.855+3618=	XM_011539558.4:c.855+3618A>C	XM_011539558.4:c.855+3618A>G
TBC1D12 transcript variant X6	XM_017015998.3:c.492+3618=	XM_017015998.3:c.492+3618A>C	XM_017015998.3:c.492+3618A>G
TBC1D12 transcript variant X8	XM_017015999.3:c.492+3618=	XM_017015999.3:c.492+3618A>C	XM_017015999.3:c.492+3618A>G
TBC1D12 transcript variant X2	XM_047424905.1:c.1761+3618=	XM_047424905.1:c.1761+3618A>C	XM_047424905.1:c.1761+3618A>G
TBC1D12 transcript variant X7	XM_047424907.1:c.492+3618=	XM_047424907.1:c.492+3618A>C	XM_047424907.1:c.492+3618A>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#.

70 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss16480807	Feb 27, 2004 (120)
2	SC_SNP	ss18424127	Feb 27, 2004 (120)
3	SSAHASNP	ss20678625	Apr 05, 2004 (121)
4	HGSV	ss79688322	Dec 14, 2007 (130)
5	BGI	ss102902567	Dec 01, 2009 (131)
6	1000GENOMES	ss109667179	Jan 24, 2009 (130)
7	ILLUMINA-UK	ss119274695	Dec 01, 2009 (131)
8	ENSEMBL	ss144236865	Dec 01, 2009 (131)
9	GMI	ss155405937	Dec 01, 2009 (131)
10	ILLUMINA	ss161036083	Dec 01, 2009 (131)
11	BUSHMAN	ss201883391	Jul 04, 2010 (132)
12	BCM-HGSC-SUB	ss207322586	Jul 04, 2010 (132)
13	1000GENOMES	ss211025178	Jul 14, 2010 (132)
14	1000GENOMES	ss224883489	Jul 14, 2010 (132)
15	1000GENOMES	ss235292086	Jul 15, 2010 (132)
16	1000GENOMES	ss241975405	Jul 15, 2010 (132)
17	BL	ss254533510	May 09, 2011 (134)
18	GMI	ss280731706	May 04, 2012 (137)
19	PJP	ss290908959	May 09, 2011 (134)
20	ILLUMINA	ss479406610	Sep 08, 2015 (146)
21	TISHKOFF	ss562142058	Apr 25, 2013 (138)
22	SSMP	ss657181581	Apr 25, 2013 (138)
23	EVA-GONL	ss987802498	Aug 21, 2014 (142)
24	1000GENOMES	ss1338615702	Aug 21, 2014 (142)
25	EVA_GENOME_DK	ss1575296127	Apr 01, 2015 (144)
26	EVA_DECODE	ss1597475787	Apr 01, 2015 (144)
27	EVA_UK10K_ALSPAC	ss1625192127	Apr 01, 2015 (144)
28	EVA_UK10K_TWINSUK	ss1668186160	Apr 01, 2015 (144)
29	HAMMER_LAB	ss1806520218	Sep 08, 2015 (146)
30	WEILL_CORNELL_DGM	ss1931168505	Feb 12, 2016 (147)
31	GENOMED	ss1967199641	Jul 19, 2016 (147)
32	JJLAB	ss2026312897	Sep 14, 2016 (149)
33	USC_VALOUEV	ss2154589321	Nov 08, 2017 (151)
34	HUMAN_LONGEVITY	ss2177133517	Dec 20, 2016 (150)
35	SYSTEMSBIOZJU	ss2627625296	Nov 08, 2017 (151)
36	GRF	ss2698841955	Nov 08, 2017 (151)
37	GNOMAD	ss2892106724	Nov 08, 2017 (151)
38	SWEGEN	ss3006962866	Nov 08, 2017 (151)
39	BIOINF_KMB_FNS_UNIBA	ss3026946579	Nov 08, 2017 (151)
40	CSHL	ss3349260575	Nov 08, 2017 (151)
41	ILLUMINA	ss3636101510	Oct 12, 2018 (152)
42	URBANLAB	ss3649441179	Oct 12, 2018 (152)
43	EGCUT_WGS	ss3674375134	Jul 13, 2019 (153)
44	EVA_DECODE	ss3690458357	Jul 13, 2019 (153)
45	ACPOP	ss3737583949	Jul 13, 2019 (153)
46	EVA	ss3748466222	Jul 13, 2019 (153)
47	PACBIO	ss3786756645	Jul 13, 2019 (153)
48	PACBIO	ss3791924148	Jul 13, 2019 (153)
49	PACBIO	ss3796806267	Jul 13, 2019 (153)
50	KHV_HUMAN_GENOMES	ss3813832184	Jul 13, 2019 (153)
51	EVA	ss3832276282	Apr 26, 2020 (154)
52	EVA	ss3839679215	Apr 26, 2020 (154)
53	EVA	ss3845152876	Apr 26, 2020 (154)
54	SGDP_PRJ	ss3874823841	Apr 26, 2020 (154)
55	KRGDB	ss3922951317	Apr 26, 2020 (154)
56	KOGIC	ss3968454777	Apr 26, 2020 (154)
57	TOPMED	ss4862559981	Apr 27, 2021 (155)
58	TOMMO_GENOMICS	ss5198960584	Apr 27, 2021 (155)
59	1000G_HIGH_COVERAGE	ss5285081282	Oct 16, 2022 (156)
60	EVA	ss5395312284	Oct 16, 2022 (156)
61	HUGCELL_USP	ss5480542218	Oct 16, 2022 (156)
62	EVA	ss5510128470	Oct 16, 2022 (156)
63	1000G_HIGH_COVERAGE	ss5579554636	Oct 16, 2022 (156)
64	SANFORD_IMAGENETICS	ss5649882271	Oct 16, 2022 (156)
65	TOMMO_GENOMICS	ss5745175690	Oct 16, 2022 (156)
66	YY_MCH	ss5811790759	Oct 16, 2022 (156)
67	EVA	ss5824805316	Oct 16, 2022 (156)
68	EVA	ss5849696556	Oct 16, 2022 (156)
69	EVA	ss5880078281	Oct 16, 2022 (156)
70	EVA	ss5941168620	Oct 16, 2022 (156)
71	1000Genomes	NC_000010.10 - 96275029	Oct 12, 2018 (152)
72	1000Genomes_30x	NC_000010.11 - 94515272	Oct 16, 2022 (156)
73	The Avon Longitudinal Study of Parents and Children	NC_000010.10 - 96275029	Oct 12, 2018 (152)
74	Genetic variation in the Estonian population	NC_000010.10 - 96275029	Oct 12, 2018 (152)
75	The Danish reference pan genome	NC_000010.10 - 96275029	Apr 26, 2020 (154)
76	gnomAD - Genomes	NC_000010.11 - 94515272	Apr 27, 2021 (155)
77	Genome of the Netherlands Release 5	NC_000010.10 - 96275029	Apr 26, 2020 (154)
78	KOREAN population from KRGDB	NC_000010.10 - 96275029	Apr 26, 2020 (154)
79	Korean Genome Project	NC_000010.11 - 94515272	Apr 26, 2020 (154)
80	Northern Sweden	NC_000010.10 - 96275029	Jul 13, 2019 (153)
81	Qatari	NC_000010.10 - 96275029	Apr 26, 2020 (154)
82	SGDP_PRJ	NC_000010.10 - 96275029	Apr 26, 2020 (154)
83	Siberian	NC_000010.10 - 96275029	Apr 26, 2020 (154)
84	8.3KJPN	NC_000010.10 - 96275029	Apr 27, 2021 (155)
85	14KJPN	NC_000010.11 - 94515272	Oct 16, 2022 (156)
86	TopMed	NC_000010.11 - 94515272	Apr 27, 2021 (155)
87	UK 10K study - Twins	NC_000010.10 - 96275029	Oct 12, 2018 (152)
88	ALFA	NC_000010.11 - 94515272	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)
rs57388150	May 23, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss79688322	NC_000010.8:96265018:A:C	NC_000010.11:94515271:A:C	(self)
ss109667179, ss119274695, ss201883391, ss207322586, ss211025178, ss254533510, ss280731706, ss290908959, ss1597475787	NC_000010.9:96265018:A:C	NC_000010.11:94515271:A:C	(self)
51046858, 28341295, 20113382, 2282289, 12637408, 30128711, 10868814, 13210435, 26840821, 7105675, 56929891, 28341295, ss224883489, ss235292086, ss241975405, ss479406610, ss562142058, ss657181581, ss987802498, ss1338615702, ss1575296127, ss1625192127, ss1668186160, ss1806520218, ss1931168505, ss1967199641, ss2026312897, ss2154589321, ss2627625296, ss2698841955, ss2892106724, ss3006962866, ss3349260575, ss3636101510, ss3674375134, ss3737583949, ss3748466222, ss3786756645, ss3791924148, ss3796806267, ss3832276282, ss3839679215, ss3874823841, ss3922951317, ss5198960584, ss5395312284, ss5510128470, ss5649882271, ss5824805316, ss5941168620	NC_000010.10:96275028:A:C	NC_000010.11:94515271:A:C	(self)
67080571, 360681796, 24832778, 79012794, 78105636, 290639875, ss2177133517, ss3026946579, ss3649441179, ss3690458357, ss3813832184, ss3845152876, ss3968454777, ss4862559981, ss5285081282, ss5480542218, ss5579554636, ss5745175690, ss5811790759, ss5849696556, ss5880078281	NC_000010.11:94515271:A:C	NC_000010.11:94515271:A:C	(self)
ss16480807, ss18424127, ss20678625	NT_030059.11:15023554:A:C	NC_000010.11:94515271:A:C	(self)
ss102902567, ss144236865, ss155405937, ss161036083	NT_030059.13:47079492:A:C	NC_000010.11:94515271:A:C	(self)
30128711, ss3922951317	NC_000010.10:96275028:A:G	NC_000010.11:94515271:A: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 rs11187996

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

rs11187996