Name: rs648104
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.

rs648104

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr18:42772911 (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: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.028849 (7636/264690, TOPMED)
T=0.00004 (1/28258, 14KJPN)
T=0.00392 (72/18376, ALFA) (+ 13 more)
T=0.00000 (0/16760, 8.3KJPN)
T=0.0255 (163/6404, 1000G_30x)
T=0.0262 (131/5008, 1000G)
T=0.0003 (1/3854, ALSPAC)
T=0.0003 (1/3708, TWINSUK)
T=0.0003 (1/2930, KOREAN)
T=0.0000 (0/1832, Korea1K)
T=0.000 (0/600, NorthernSweden)
T=0.023 (13/558, SGDP_PRJ)
T=0.009 (2/216, Qatari)
T=0.000 (0/212, Vietnamese)
T=0.00 (0/54, Siberian)
T=0.00 (0/40, 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	18376	T=0.00392	A=0.00000, C=0.99608
European	Sub	17112	T=0.00018	A=0.00000, C=0.99982
African	Sub	376	T=0.152	A=0.000, C=0.848
African Others	Sub	16	T=0.06	A=0.00, C=0.94
African American	Sub	360	T=0.156	A=0.000, C=0.844
Asian	Sub	20	T=0.00	A=0.00, C=1.00
East Asian	Sub	16	T=0.00	A=0.00, C=1.00
Other Asian	Sub	4	T=0.0	A=0.0, C=1.0
Latin American 1	Sub	22	T=0.00	A=0.00, C=1.00
Latin American 2	Sub	90	T=0.01	A=0.00, C=0.99
South Asian	Sub	20	T=0.00	A=0.00, C=1.00
Other	Sub	736	T=0.015	A=0.000, C=0.985

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	T=0.028849	C=0.971151
14KJPN	JAPANESE	Study-wide	28258	T=0.00004	C=0.99996
Allele Frequency Aggregator	Total	Global	18376	T=0.00392	A=0.00000, C=0.99608
Allele Frequency Aggregator	European	Sub	17112	T=0.00018	A=0.00000, C=0.99982
Allele Frequency Aggregator	Other	Sub	736	T=0.015	A=0.000, C=0.985
Allele Frequency Aggregator	African	Sub	376	T=0.152	A=0.000, C=0.848
Allele Frequency Aggregator	Latin American 2	Sub	90	T=0.01	A=0.00, C=0.99
Allele Frequency Aggregator	Latin American 1	Sub	22	T=0.00	A=0.00, C=1.00
Allele Frequency Aggregator	South Asian	Sub	20	T=0.00	A=0.00, C=1.00
Allele Frequency Aggregator	Asian	Sub	20	T=0.00	A=0.00, C=1.00
8.3KJPN	JAPANESE	Study-wide	16760	T=0.00000	C=1.00000
1000Genomes_30x	Global	Study-wide	6404	T=0.0255	C=0.9745
1000Genomes_30x	African	Sub	1786	T=0.0840	C=0.9160
1000Genomes_30x	Europe	Sub	1266	T=0.0024	C=0.9976
1000Genomes_30x	South Asian	Sub	1202	T=0.0000	C=1.0000
1000Genomes_30x	East Asian	Sub	1170	T=0.0000	C=1.0000
1000Genomes_30x	American	Sub	980	T=0.010	C=0.990
1000Genomes	Global	Study-wide	5008	T=0.0262	C=0.9738
1000Genomes	African	Sub	1322	T=0.0930	C=0.9070
1000Genomes	East Asian	Sub	1008	T=0.0000	C=1.0000
1000Genomes	Europe	Sub	1006	T=0.0020	C=0.9980
1000Genomes	South Asian	Sub	978	T=0.000	C=1.000
1000Genomes	American	Sub	694	T=0.009	C=0.991
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.0003	C=0.9997
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.0003	C=0.9997
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.0003	A=0.0000, C=0.9997
Korean Genome Project	KOREAN	Study-wide	1832	T=0.0000	C=1.0000
Northern Sweden	ACPOP	Study-wide	600	T=0.000	C=1.000
SGDP_PRJ	Global	Study-wide	558	T=0.023	C=0.977
Qatari	Global	Study-wide	216	T=0.009	C=0.991
A Vietnamese Genetic Variation Database	Global	Study-wide	212	T=0.000	C=1.000
Siberian	Global	Study-wide	54	T=0.00	C=1.00
The Danish reference pan genome	Danish	Study-wide	40	T=0.00	C=1.00

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.42772911T>A
GRCh38.p14 chr 18	NC_000018.10:g.42772911T>C
GRCh37.p13 chr 18	NC_000018.9:g.40352876T>A
GRCh37.p13 chr 18	NC_000018.9:g.40352876T>C

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.29-2919… NM_001272077.2:c.29-29191A>T	N/A	Intron Variant
RIT2 transcript variant 1	NM_002930.4:c.427-29191A>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	T=	A	C
GRCh38.p14 chr 18	NC_000018.10:g.42772911=	NC_000018.10:g.42772911T>A	NC_000018.10:g.42772911T>C
GRCh37.p13 chr 18	NC_000018.9:g.40352876=	NC_000018.9:g.40352876T>A	NC_000018.9:g.40352876T>C
RIT2 transcript variant 2	NM_001272077.1:c.*29-29191=	NM_001272077.1:c.*29-29191A>T	NM_001272077.1:c.*29-29191A>G
RIT2 transcript variant 2	NM_001272077.2:c.*29-29191=	NM_001272077.2:c.*29-29191A>T	NM_001272077.2:c.*29-29191A>G
RIT2 transcript variant 1	NM_002930.3:c.427-29191=	NM_002930.3:c.427-29191A>T	NM_002930.3:c.427-29191A>G
RIT2 transcript variant 1	NM_002930.4:c.427-29191=	NM_002930.4:c.427-29191A>T	NM_002930.4:c.427-29191A>G
RIT2 transcript variant X1	XM_005258327.1:c.370-29191=	XM_005258327.1:c.370-29191A>T	XM_005258327.1:c.370-29191A>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#.

84 SubSNP, 18 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss821012	Aug 11, 2000 (83)
2	TSC-CSHL	ss2381672	Oct 23, 2000 (88)
3	SSAHASNP	ss21472024	Apr 05, 2004 (121)
4	ABI	ss44117917	Mar 13, 2006 (126)
5	BCMHGSC_JDW	ss90774489	Mar 24, 2008 (129)
6	HUMANGENOME_JCVI	ss96337834	Feb 04, 2009 (130)
7	BGI	ss106542102	Feb 04, 2009 (130)
8	1000GENOMES	ss110440015	Jan 24, 2009 (130)
9	1000GENOMES	ss114319484	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss117855203	Feb 14, 2009 (130)
11	ENSEMBL	ss136426164	Dec 01, 2009 (131)
12	ENSEMBL	ss137354111	Dec 01, 2009 (131)
13	GMI	ss155096903	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss168127321	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss169651566	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss171737518	Jul 04, 2010 (132)
17	BUSHMAN	ss203206346	Jul 04, 2010 (132)
18	BCM-HGSC-SUB	ss208123241	Jul 04, 2010 (132)
19	1000GENOMES	ss227839233	Jul 14, 2010 (132)
20	1000GENOMES	ss237450579	Jul 15, 2010 (132)
21	1000GENOMES	ss243703216	Jul 15, 2010 (132)
22	BL	ss255623189	May 09, 2011 (134)
23	GMI	ss282975966	May 04, 2012 (137)
24	GMI	ss287276462	Apr 25, 2013 (138)
25	PJP	ss292163125	May 09, 2011 (134)
26	ILLUMINA	ss483368239	May 04, 2012 (137)
27	ILLUMINA	ss483725564	May 04, 2012 (137)
28	ILLUMINA	ss535581474	Sep 08, 2015 (146)
29	TISHKOFF	ss565618133	Apr 25, 2013 (138)
30	SSMP	ss661448093	Apr 25, 2013 (138)
31	ILLUMINA	ss780251100	Aug 21, 2014 (142)
32	ILLUMINA	ss782127285	Aug 21, 2014 (142)
33	ILLUMINA	ss835736762	Aug 21, 2014 (142)
34	JMKIDD_LAB	ss1081471695	Aug 21, 2014 (142)
35	1000GENOMES	ss1360880760	Aug 21, 2014 (142)
36	DDI	ss1428204976	Apr 01, 2015 (144)
37	EVA_GENOME_DK	ss1578387259	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1636793052	Apr 01, 2015 (144)
39	EVA_UK10K_TWINSUK	ss1679787085	Apr 01, 2015 (144)
40	HAMMER_LAB	ss1809034929	Sep 08, 2015 (146)
41	WEILL_CORNELL_DGM	ss1937157555	Feb 12, 2016 (147)
42	GENOMED	ss1968514827	Jul 19, 2016 (147)
43	JJLAB	ss2029348038	Sep 14, 2016 (149)
44	USC_VALOUEV	ss2157852471	Dec 20, 2016 (150)
45	HUMAN_LONGEVITY	ss2221271268	Dec 20, 2016 (150)
46	SYSTEMSBIOZJU	ss2629172205	Nov 08, 2017 (151)
47	ILLUMINA	ss2633468272	Nov 08, 2017 (151)
48	GRF	ss2702438447	Nov 08, 2017 (151)
49	GNOMAD	ss2956282297	Nov 08, 2017 (151)
50	SWEGEN	ss3016467934	Nov 08, 2017 (151)
51	BIOINF_KMB_FNS_UNIBA	ss3028501561	Nov 08, 2017 (151)
52	CSHL	ss3352006060	Nov 08, 2017 (151)
53	ILLUMINA	ss3627800375	Oct 12, 2018 (152)
54	ILLUMINA	ss3631445081	Oct 12, 2018 (152)
55	ILLUMINA	ss3642025715	Oct 12, 2018 (152)
56	URBANLAB	ss3650782744	Oct 12, 2018 (152)
57	EVA_DECODE	ss3701587502	Jul 13, 2019 (153)
58	ACPOP	ss3742511689	Jul 13, 2019 (153)
59	EVA	ss3755342618	Jul 13, 2019 (153)
60	PACBIO	ss3788360508	Jul 13, 2019 (153)
61	PACBIO	ss3793293023	Jul 13, 2019 (153)
62	PACBIO	ss3798179369	Jul 13, 2019 (153)
63	KHV_HUMAN_GENOMES	ss3820607730	Jul 13, 2019 (153)
64	EVA	ss3835150895	Apr 27, 2020 (154)
65	EVA	ss3841192632	Apr 27, 2020 (154)
66	EVA	ss3846694630	Apr 27, 2020 (154)
67	SGDP_PRJ	ss3886944938	Apr 27, 2020 (154)
68	KRGDB	ss3936806944	Apr 27, 2020 (154)
69	KOGIC	ss3980081543	Apr 27, 2020 (154)
70	TOPMED	ss5055425377	Apr 26, 2021 (155)
71	TOMMO_GENOMICS	ss5225009783	Apr 26, 2021 (155)
72	1000G_HIGH_COVERAGE	ss5305169501	Oct 16, 2022 (156)
73	EVA	ss5315930160	Oct 16, 2022 (156)
74	EVA	ss5431190874	Oct 16, 2022 (156)
75	HUGCELL_USP	ss5497952796	Oct 16, 2022 (156)
76	EVA	ss5511925050	Oct 16, 2022 (156)
77	1000G_HIGH_COVERAGE	ss5609946625	Oct 16, 2022 (156)
78	SANFORD_IMAGENETICS	ss5661225152	Oct 16, 2022 (156)
79	TOMMO_GENOMICS	ss5782754991	Oct 16, 2022 (156)
80	YY_MCH	ss5817065376	Oct 16, 2022 (156)
81	EVA	ss5827494104	Oct 16, 2022 (156)
82	EVA	ss5852037650	Oct 16, 2022 (156)
83	EVA	ss5873937186	Oct 16, 2022 (156)
84	EVA	ss5952634499	Oct 16, 2022 (156)
85	1000Genomes	NC_000018.9 - 40352876	Oct 12, 2018 (152)
86	1000Genomes_30x	NC_000018.10 - 42772911	Oct 16, 2022 (156)
87	The Avon Longitudinal Study of Parents and Children	NC_000018.9 - 40352876	Oct 12, 2018 (152)
88	The Danish reference pan genome	NC_000018.9 - 40352876	Apr 27, 2020 (154)
89	gnomAD - Genomes Submission ignored due to conflicting rows: Row 523500829 (NC_000018.10:42772910:T:A 1/140200) Row 523500830 (NC_000018.10:42772910:T:C 136319/140194)	-	Apr 26, 2021 (155)
90	gnomAD - Genomes Submission ignored due to conflicting rows: Row 523500829 (NC_000018.10:42772910:T:A 1/140200) Row 523500830 (NC_000018.10:42772910:T:C 136319/140194)	-	Apr 26, 2021 (155)
91	KOREAN population from KRGDB	NC_000018.9 - 40352876	Apr 27, 2020 (154)
92	Korean Genome Project	NC_000018.10 - 42772911	Apr 27, 2020 (154)
93	Northern Sweden	NC_000018.9 - 40352876	Jul 13, 2019 (153)
94	Qatari	NC_000018.9 - 40352876	Apr 27, 2020 (154)
95	SGDP_PRJ	NC_000018.9 - 40352876	Apr 27, 2020 (154)
96	Siberian	NC_000018.9 - 40352876	Apr 27, 2020 (154)
97	8.3KJPN	NC_000018.9 - 40352876	Apr 26, 2021 (155)
98	14KJPN	NC_000018.10 - 42772911	Oct 16, 2022 (156)
99	TopMed	NC_000018.10 - 42772911	Apr 26, 2021 (155)
100	UK 10K study - Twins	NC_000018.9 - 40352876	Oct 12, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000018.9 - 40352876	Jul 13, 2019 (153)
102	ALFA	NC_000018.10 - 42772911	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
43984338, ss3936806944	NC_000018.9:40352875:T:A	NC_000018.10:42772910:T:A	(self)
1033099451	NC_000018.10:42772910:T:A	NC_000018.10:42772910:T:A	(self)
ss90774489, ss110440015, ss114319484, ss117855203, ss168127321, ss169651566, ss171737518, ss203206346, ss208123241, ss255623189, ss282975966, ss287276462, ss292163125, ss483725564	NC_000018.8:38606873:T:C	NC_000018.10:42772910:T:C	(self)
74205172, 41109096, 4579963, 43984338, 15796554, 19199477, 38961918, 10368825, 82979090, 41109096, 9083517, ss227839233, ss237450579, ss243703216, ss483368239, ss535581474, ss565618133, ss661448093, ss780251100, ss782127285, ss835736762, ss1081471695, ss1360880760, ss1428204976, ss1578387259, ss1636793052, ss1679787085, ss1809034929, ss1937157555, ss1968514827, ss2029348038, ss2157852471, ss2629172205, ss2633468272, ss2702438447, ss2956282297, ss3016467934, ss3352006060, ss3627800375, ss3631445081, ss3642025715, ss3742511689, ss3755342618, ss3788360508, ss3793293023, ss3798179369, ss3835150895, ss3841192632, ss3886944938, ss3936806944, ss5225009783, ss5315930160, ss5431190874, ss5511925050, ss5661225152, ss5827494104, ss5952634499	NC_000018.9:40352875:T:C	NC_000018.10:42772910:T:C	(self)
97472560, 36459544, 116592095, 270971040, 1033099451, ss2221271268, ss3028501561, ss3650782744, ss3701587502, ss3820607730, ss3846694630, ss3980081543, ss5055425377, ss5305169501, ss5497952796, ss5609946625, ss5782754991, ss5817065376, ss5852037650, ss5873937186	NC_000018.10:42772910:T:C	NC_000018.10:42772910:T:C	(self)
ss21472024	NT_010966.13:21841977:T:C	NC_000018.10:42772910:T:C	(self)
ss821012, ss2381672, ss44117917, ss96337834, ss106542102, ss136426164, ss137354111, ss155096903	NT_010966.14:21841977:T:C	NC_000018.10:42772910:T: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 rs648104

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

rs648104