Name: rs11460196
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.

rs11460196

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr18:42783544-42783549 (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: delT / dupT / dupTT
Variation Type: Indel Insertion and Deletion
Frequency: dupT=0.45714 (12918/28258, 14KJPN)
dupT=0.45758 (7669/16760, 8.3KJPN)
dupT=0.07881 (963/12220, ALFA) (+ 9 more)
dupT=0.4252 (2723/6404, 1000G_30x)
dupT=0.4173 (2090/5008, 1000G)
dupT=0.2150 (963/4480, Estonian)
dupT=0.1796 (692/3854, ALSPAC)
dupT=0.1893 (702/3708, TWINSUK)
dupT=0.4514 (827/1832, Korea1K)
dupT=0.201 (201/998, GoNL)
dupT=0.197 (118/600, NorthernSweden)
dupT=0.20 (8/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RIT2 : 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	12220	TTTTTT=0.92119	TTTTT=0.00000, TTTTTTT=0.07881, TTTTTTTT=0.00000
European	Sub	11102	TTTTTT=0.91344	TTTTT=0.00000, TTTTTTT=0.08656, TTTTTTTT=0.00000
African	Sub	456	TTTTTT=1.000	TTTTT=0.000, TTTTTTT=0.000, TTTTTTTT=0.000
African Others	Sub	8	TTTTTT=1.0	TTTTT=0.0, TTTTTTT=0.0, TTTTTTTT=0.0
African American	Sub	448	TTTTTT=1.000	TTTTT=0.000, TTTTTTT=0.000, TTTTTTTT=0.000
Asian	Sub	32	TTTTTT=1.00	TTTTT=0.00, TTTTTTT=0.00, TTTTTTTT=0.00
East Asian	Sub	22	TTTTTT=1.00	TTTTT=0.00, TTTTTTT=0.00, TTTTTTTT=0.00
Other Asian	Sub	10	TTTTTT=1.0	TTTTT=0.0, TTTTTTT=0.0, TTTTTTTT=0.0
Latin American 1	Sub	64	TTTTTT=1.00	TTTTT=0.00, TTTTTTT=0.00, TTTTTTTT=0.00
Latin American 2	Sub	268	TTTTTT=1.000	TTTTT=0.000, TTTTTTT=0.000, TTTTTTTT=0.000
South Asian	Sub	46	TTTTTT=1.00	TTTTT=0.00, TTTTTTT=0.00, TTTTTTTT=0.00
Other	Sub	252	TTTTTT=0.992	TTTTT=0.000, TTTTTTT=0.008, TTTTTTTT=0.000

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
14KJPN	JAPANESE	Study-wide	28258	- No frequency provided	dupT=0.45714
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupT=0.45758
Allele Frequency Aggregator	Total	Global	12220	(T)₆=0.92119	delT=0.00000, dupT=0.07881, dupTT=0.00000
Allele Frequency Aggregator	European	Sub	11102	(T)₆=0.91344	delT=0.00000, dupT=0.08656, dupTT=0.00000
Allele Frequency Aggregator	African	Sub	456	(T)₆=1.000	delT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator	Latin American 2	Sub	268	(T)₆=1.000	delT=0.000, dupT=0.000, dupTT=0.000
Allele Frequency Aggregator	Other	Sub	252	(T)₆=0.992	delT=0.000, dupT=0.008, dupTT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	64	(T)₆=1.00	delT=0.00, dupT=0.00, dupTT=0.00
Allele Frequency Aggregator	South Asian	Sub	46	(T)₆=1.00	delT=0.00, dupT=0.00, dupTT=0.00
Allele Frequency Aggregator	Asian	Sub	32	(T)₆=1.00	delT=0.00, dupT=0.00, dupTT=0.00
1000Genomes_30x	Global	Study-wide	6404	- No frequency provided	dupT=0.4252
1000Genomes_30x	African	Sub	1786	- No frequency provided	dupT=0.6926
1000Genomes_30x	Europe	Sub	1266	- No frequency provided	dupT=0.1777
1000Genomes_30x	South Asian	Sub	1202	- No frequency provided	dupT=0.3336
1000Genomes_30x	East Asian	Sub	1170	- No frequency provided	dupT=0.4453
1000Genomes_30x	American	Sub	980	- No frequency provided	dupT=0.346
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupT=0.4173
1000Genomes	African	Sub	1322	- No frequency provided	dupT=0.6831
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupT=0.4335
1000Genomes	Europe	Sub	1006	- No frequency provided	dupT=0.1829
1000Genomes	South Asian	Sub	978	- No frequency provided	dupT=0.337
1000Genomes	American	Sub	694	- No frequency provided	dupT=0.340
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	dupT=0.2150
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	- No frequency provided	dupT=0.1796
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	- No frequency provided	dupT=0.1893
Korean Genome Project	KOREAN	Study-wide	1832	- No frequency provided	dupT=0.4514
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	- No frequency provided	dupT=0.201
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupT=0.197
The Danish reference pan genome	Danish	Study-wide	40	- No frequency provided	dupT=0.20

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 18	NC_000018.10:g.42783549del
GRCh38.p14 chr 18	NC_000018.10:g.42783549dup
GRCh38.p14 chr 18	NC_000018.10:g.42783548_42783549dup
GRCh37.p13 chr 18	NC_000018.9:g.40363514del
GRCh37.p13 chr 18	NC_000018.9:g.40363514dup
GRCh37.p13 chr 18	NC_000018.9:g.40363513_40363514dup

Gene: RIT2, Ras like without CAAX 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RIT2 transcript variant 2	NM_001272077.2:c.29-3982… NM_001272077.2:c.29-39824del	N/A	Intron Variant
RIT2 transcript variant 1	NM_002930.4:c.427-39824del	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	(T)₆=	delT	dupT	dupTT
GRCh38.p14 chr 18	NC_000018.10:g.42783544_42783549=	NC_000018.10:g.42783549del	NC_000018.10:g.42783549dup	NC_000018.10:g.42783548_42783549dup
GRCh37.p13 chr 18	NC_000018.9:g.40363509_40363514=	NC_000018.9:g.40363514del	NC_000018.9:g.40363514dup	NC_000018.9:g.40363513_40363514dup
RIT2 transcript variant 2	NM_001272077.1:c.*29-39824=	NM_001272077.1:c.*29-39824del	NM_001272077.1:c.*29-39824dup	NM_001272077.1:c.29-39825_29-39824dup
RIT2 transcript variant 2	NM_001272077.2:c.*29-39824=	NM_001272077.2:c.*29-39824del	NM_001272077.2:c.*29-39824dup	NM_001272077.2:c.29-39825_29-39824dup
RIT2 transcript variant 1	NM_002930.3:c.427-39824=	NM_002930.3:c.427-39824del	NM_002930.3:c.427-39824dup	NM_002930.3:c.427-39825_427-39824dup
RIT2 transcript variant 1	NM_002930.4:c.427-39824=	NM_002930.4:c.427-39824del	NM_002930.4:c.427-39824dup	NM_002930.4:c.427-39825_427-39824dup
RIT2 transcript variant X1	XM_005258327.1:c.370-39824=	XM_005258327.1:c.370-39824del	XM_005258327.1:c.370-39824dup	XM_005258327.1:c.370-39825_370-39824dup

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#.

49 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GMI	ss155735148	Dec 01, 2009 (138)
2	BUSHMAN	ss193478366	Jul 04, 2010 (138)
3	GMI	ss288508279	Oct 12, 2018 (152)
4	GMI	ss289358080	May 04, 2012 (138)
5	GMI	ss289358081	May 04, 2012 (137)
6	1000GENOMES	ss327842841	May 09, 2011 (138)
7	1000GENOMES	ss327972359	May 09, 2011 (138)
8	1000GENOMES	ss328247569	May 09, 2011 (138)
9	1000GENOMES	ss499408270	May 04, 2012 (138)
10	LUNTER	ss552570087	Apr 25, 2013 (138)
11	LUNTER	ss552941497	Apr 25, 2013 (138)
12	LUNTER	ss553639866	Apr 25, 2013 (138)
13	SSMP	ss664399022	Apr 01, 2015 (144)
14	EVA-GONL	ss993688893	Aug 21, 2014 (142)
15	1000GENOMES	ss1377409063	Aug 21, 2014 (142)
16	EVA_GENOME_DK	ss1575145678	Apr 01, 2015 (144)
17	EVA_DECODE	ss1697745435	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1708976595	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1708976852	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1809034956	Sep 08, 2015 (146)
21	JJLAB	ss2031369882	Sep 14, 2016 (149)
22	SYSTEMSBIOZJU	ss2629172222	Nov 08, 2017 (151)
23	SWEGEN	ss3016468046	Nov 08, 2017 (151)
24	MCHAISSO	ss3063891645	Nov 08, 2017 (151)
25	MCHAISSO	ss3065681174	Nov 08, 2017 (151)
26	BIOINF_KMB_FNS_UNIBA	ss3645485180	Oct 12, 2018 (152)
27	EGCUT_WGS	ss3683306609	Jul 13, 2019 (153)
28	EVA_DECODE	ss3701587639	Jul 13, 2019 (153)
29	ACPOP	ss3742511747	Jul 13, 2019 (153)
30	KHV_HUMAN_GENOMES	ss3820607789	Jul 13, 2019 (153)
31	EVA	ss3835150924	Apr 27, 2020 (154)
32	EVA	ss3841192652	Apr 27, 2020 (154)
33	EVA	ss3846694650	Apr 27, 2020 (154)
34	KOGIC	ss3980081661	Apr 27, 2020 (154)
35	GNOMAD	ss4321409213	Apr 26, 2021 (155)
36	GNOMAD	ss4321409214	Apr 26, 2021 (155)
37	GNOMAD	ss4321409215	Apr 26, 2021 (155)
38	TOMMO_GENOMICS	ss5225010061	Apr 26, 2021 (155)
39	1000G_HIGH_COVERAGE	ss5305169708	Oct 16, 2022 (156)
40	HUGCELL_USP	ss5497953005	Oct 16, 2022 (156)
41	EVA	ss5511925078	Oct 16, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5609946995	Oct 16, 2022 (156)
43	SANFORD_IMAGENETICS	ss5661225261	Oct 16, 2022 (156)
44	TOMMO_GENOMICS	ss5782755363	Oct 16, 2022 (156)
45	YY_MCH	ss5817065417	Oct 16, 2022 (156)
46	EVA	ss5827494191	Oct 16, 2022 (156)
47	EVA	ss5852037676	Oct 16, 2022 (156)
48	EVA	ss5873937432	Oct 16, 2022 (156)
49	EVA	ss5952634615	Oct 16, 2022 (156)
50	1000Genomes	NC_000018.9 - 40363509	Oct 12, 2018 (152)
51	1000Genomes_30x	NC_000018.10 - 42783544	Oct 16, 2022 (156)
52	The Avon Longitudinal Study of Parents and Children	NC_000018.9 - 40363509	Oct 12, 2018 (152)
53	Genetic variation in the Estonian population	NC_000018.9 - 40363509	Oct 12, 2018 (152)
54	The Danish reference pan genome	NC_000018.9 - 40363509	Apr 27, 2020 (154)
55	gnomAD - Genomes Submission ignored due to conflicting rows: Row 523503001 (NC_000018.10:42783543::T 45834/139912) Row 523503002 (NC_000018.10:42783543::TT 1/139960) Row 523503003 (NC_000018.10:42783543:T: 1/139960)	-	Apr 26, 2021 (155)
56	gnomAD - Genomes Submission ignored due to conflicting rows: Row 523503001 (NC_000018.10:42783543::T 45834/139912) Row 523503002 (NC_000018.10:42783543::TT 1/139960) Row 523503003 (NC_000018.10:42783543:T: 1/139960)	-	Apr 26, 2021 (155)
57	gnomAD - Genomes Submission ignored due to conflicting rows: Row 523503001 (NC_000018.10:42783543::T 45834/139912) Row 523503002 (NC_000018.10:42783543::TT 1/139960) Row 523503003 (NC_000018.10:42783543:T: 1/139960)	-	Apr 26, 2021 (155)
58	Genome of the Netherlands Release 5	NC_000018.9 - 40363509	Apr 27, 2020 (154)
59	Korean Genome Project	NC_000018.10 - 42783544	Apr 27, 2020 (154)
60	Northern Sweden	NC_000018.9 - 40363509	Jul 13, 2019 (153)
61	8.3KJPN	NC_000018.9 - 40363509	Apr 26, 2021 (155)
62	14KJPN	NC_000018.10 - 42783544	Oct 16, 2022 (156)
63	UK 10K study - Twins	NC_000018.9 - 40363509	Oct 12, 2018 (152)
64	ALFA	NC_000018.10 - 42783544	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)
rs34667659	May 11, 2012 (137)
rs77215154	May 15, 2013 (138)
rs150024416	Sep 17, 2011 (135)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss5511925078	NC_000018.9:40363508:T:	NC_000018.10:42783543:TTTTTT:TTTTT
ss4321409215	NC_000018.10:42783543:T:	NC_000018.10:42783543:TTTTTT:TTTTT	(self)
1280345984	NC_000018.10:42783543:TTTTTT:TTTTT	NC_000018.10:42783543:TTTTTT:TTTTT	(self)
ss289358080, ss327842841, ss327972359, ss328247569, ss552570087, ss552941497, ss553639866, ss1697745435	NC_000018.8:38617506::T	NC_000018.10:42783543:TTTTTT:TTTTT… NC_000018.10:42783543:TTTTTT:TTTTTTT	(self)
ss289358081	NC_000018.8:38617512::T	NC_000018.10:42783543:TTTTTT:TTTTT… NC_000018.10:42783543:TTTTTT:TTTTTTT	(self)
74205424, 41109230, 29044857, 596197, 18317281, 15796612, 82979368, 41109230, ss499408270, ss664399022, ss993688893, ss1377409063, ss1575145678, ss1708976595, ss1708976852, ss1809034956, ss2031369882, ss2629172222, ss3016468046, ss3683306609, ss3742511747, ss3835150924, ss3841192652, ss5225010061, ss5661225261, ss5827494191, ss5952634615	NC_000018.9:40363508::T	NC_000018.10:42783543:TTTTTT:TTTTT… NC_000018.10:42783543:TTTTTT:TTTTTTT	(self)
97472930, 36459662, 116592467, ss3063891645, ss3065681174, ss3645485180, ss3701587639, ss3820607789, ss3846694650, ss3980081661, ss4321409213, ss5305169708, ss5497953005, ss5609946995, ss5782755363, ss5817065417, ss5852037676, ss5873937432	NC_000018.10:42783543::T	NC_000018.10:42783543:TTTTTT:TTTTT… NC_000018.10:42783543:TTTTTT:TTTTTTT	(self)
1280345984	NC_000018.10:42783543:TTTTTT:TTTTT… NC_000018.10:42783543:TTTTTT:TTTTTTT	NC_000018.10:42783543:TTTTTT:TTTTT… NC_000018.10:42783543:TTTTTT:TTTTTTT	(self)
ss155735148	NT_010966.14:21852610::T	NC_000018.10:42783543:TTTTTT:TTTTT… NC_000018.10:42783543:TTTTTT:TTTTTTT	(self)
ss288508279	NT_010966.14:21852616::T	NC_000018.10:42783543:TTTTTT:TTTTT… NC_000018.10:42783543:TTTTTT:TTTTTTT	(self)
ss193478366	NT_010966.15:21872337::T	NC_000018.10:42783543:TTTTTT:TTTTT… NC_000018.10:42783543:TTTTTT:TTTTTTT	(self)
ss4321409214	NC_000018.10:42783543::TT	NC_000018.10:42783543:TTTTTT:TTTTT… NC_000018.10:42783543:TTTTTT:TTTTTTTT	(self)
1280345984	NC_000018.10:42783543:TTTTTT:TTTTT… NC_000018.10:42783543:TTTTTT:TTTTTTTT	NC_000018.10:42783543:TTTTTT:TTTTT… NC_000018.10:42783543:TTTTTT:TTTTTTTT	(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 rs11460196

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
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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

rs11460196