Name: rs75164237
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.

rs75164237

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr18:42757916 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.044282 (11721/264690, TOPMED)
A=0.033436 (4686/140150, GnomAD)
A=0.29061 (8212/28258, 14KJPN) (+ 17 more)
A=0.02361 (446/18890, ALFA)
A=0.29004 (4861/16760, 8.3KJPN)
A=0.0673 (431/6404, 1000G_30x)
A=0.0715 (358/5008, 1000G)
A=0.0154 (69/4480, Estonian)
A=0.0213 (82/3854, ALSPAC)
A=0.0181 (67/3708, TWINSUK)
A=0.2720 (797/2930, KOREAN)
A=0.2773 (508/1832, Korea1K)
A=0.022 (22/998, GoNL)
A=0.057 (34/600, NorthernSweden)
A=0.005 (1/216, Qatari)
A=0.308 (66/214, Vietnamese)
T=0.45 (34/76, SGDP_PRJ)
A=0.03 (1/40, GENOME_DK)
T=0.5 (1/2, Siberian)
A=0.5 (1/2, Siberian)

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	18890	T=0.97639	A=0.02361
European	Sub	14286	T=0.98397	A=0.01603
African	Sub	2946	T=0.9837	A=0.0163
African Others	Sub	114	T=0.982	A=0.018
African American	Sub	2832	T=0.9838	A=0.0162
Asian	Sub	112	T=0.768	A=0.232
East Asian	Sub	86	T=0.78	A=0.22
Other Asian	Sub	26	T=0.73	A=0.27
Latin American 1	Sub	146	T=0.945	A=0.055
Latin American 2	Sub	610	T=0.844	A=0.156
South Asian	Sub	98	T=1.00	A=0.00
Other	Sub	692	T=0.942	A=0.058

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=0.955718	A=0.044282
gnomAD - Genomes	Global	Study-wide	140150	T=0.966564	A=0.033436
gnomAD - Genomes	European	Sub	75908	T=0.98061	A=0.01939
gnomAD - Genomes	African	Sub	42016	T=0.98529	A=0.01471
gnomAD - Genomes	American	Sub	13638	T=0.87073	A=0.12927
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	T=0.9949	A=0.0051
gnomAD - Genomes	East Asian	Sub	3118	T=0.7646	A=0.2354
gnomAD - Genomes	Other	Sub	2148	T=0.9618	A=0.0382
14KJPN	JAPANESE	Study-wide	28258	T=0.70939	A=0.29061
Allele Frequency Aggregator	Total	Global	18890	T=0.97639	A=0.02361
Allele Frequency Aggregator	European	Sub	14286	T=0.98397	A=0.01603
Allele Frequency Aggregator	African	Sub	2946	T=0.9837	A=0.0163
Allele Frequency Aggregator	Other	Sub	692	T=0.942	A=0.058
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.844	A=0.156
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.945	A=0.055
Allele Frequency Aggregator	Asian	Sub	112	T=0.768	A=0.232
Allele Frequency Aggregator	South Asian	Sub	98	T=1.00	A=0.00
8.3KJPN	JAPANESE	Study-wide	16760	T=0.70996	A=0.29004
1000Genomes_30x	Global	Study-wide	6404	T=0.9327	A=0.0673
1000Genomes_30x	African	Sub	1786	T=0.9910	A=0.0090
1000Genomes_30x	Europe	Sub	1266	T=0.9858	A=0.0142
1000Genomes_30x	South Asian	Sub	1202	T=0.9875	A=0.0125
1000Genomes_30x	East Asian	Sub	1170	T=0.7726	A=0.2274
1000Genomes_30x	American	Sub	980	T=0.882	A=0.118
1000Genomes	Global	Study-wide	5008	T=0.9285	A=0.0715
1000Genomes	African	Sub	1322	T=0.9917	A=0.0083
1000Genomes	East Asian	Sub	1008	T=0.7629	A=0.2371
1000Genomes	Europe	Sub	1006	T=0.9881	A=0.0119
1000Genomes	South Asian	Sub	978	T=0.990	A=0.010
1000Genomes	American	Sub	694	T=0.876	A=0.124
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9846	A=0.0154
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9787	A=0.0213
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9819	A=0.0181
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.7280	A=0.2720
Korean Genome Project	KOREAN	Study-wide	1832	T=0.7227	A=0.2773
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.978	A=0.022
Northern Sweden	ACPOP	Study-wide	600	T=0.943	A=0.057
Qatari	Global	Study-wide	216	T=0.995	A=0.005
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.692	A=0.308
SGDP_PRJ	Global	Study-wide	76	T=0.45	A=0.55
The Danish reference pan genome	Danish	Study-wide	40	T=0.97	A=0.03
Siberian	Global	Study-wide	2	T=0.5	A=0.5

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.42757916T>A
GRCh37.p13 chr 18	NC_000018.9:g.40337881T>A

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.29-1419… NM_001272077.2:c.29-14196A>T	N/A	Intron Variant
RIT2 transcript variant 1	NM_002930.4:c.427-14196A>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
GRCh38.p14 chr 18	NC_000018.10:g.42757916=	NC_000018.10:g.42757916T>A
GRCh37.p13 chr 18	NC_000018.9:g.40337881=	NC_000018.9:g.40337881T>A
RIT2 transcript variant 2	NM_001272077.1:c.*29-14196=	NM_001272077.1:c.*29-14196A>T
RIT2 transcript variant 2	NM_001272077.2:c.*29-14196=	NM_001272077.2:c.*29-14196A>T
RIT2 transcript variant 1	NM_002930.3:c.427-14196=	NM_002930.3:c.427-14196A>T
RIT2 transcript variant 1	NM_002930.4:c.427-14196=	NM_002930.4:c.427-14196A>T
RIT2 transcript variant X1	XM_005258327.1:c.370-14196=	XM_005258327.1:c.370-14196A>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#.

46 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GMI	ss155096778	Dec 01, 2009 (131)
2	COMPLETE_GENOMICS	ss168127089	Jul 04, 2010 (132)
3	1000GENOMES	ss237450550	Jul 15, 2010 (132)
4	1000GENOMES	ss243703193	Jul 15, 2010 (132)
5	GMI	ss282975939	May 04, 2012 (137)
6	GMI	ss287276440	Apr 25, 2013 (138)
7	SSMP	ss661448048	Apr 25, 2013 (138)
8	EVA-GONL	ss993688730	Aug 21, 2014 (142)
9	JMKIDD_LAB	ss1081471623	Aug 21, 2014 (142)
10	1000GENOMES	ss1360880347	Aug 21, 2014 (142)
11	EVA_GENOME_DK	ss1578387226	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1636792825	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1679786858	Apr 01, 2015 (144)
14	EVA_DECODE	ss1697745251	Apr 01, 2015 (144)
15	WEILL_CORNELL_DGM	ss1937157460	Feb 12, 2016 (147)
16	GENOMED	ss1968514805	Jul 19, 2016 (147)
17	JJLAB	ss2029347991	Sep 14, 2016 (149)
18	USC_VALOUEV	ss2157852423	Dec 20, 2016 (150)
19	HUMAN_LONGEVITY	ss2221270455	Dec 20, 2016 (150)
20	SYSTEMSBIOZJU	ss2629172183	Nov 08, 2017 (151)
21	GRF	ss2702438401	Nov 08, 2017 (151)
22	GNOMAD	ss2956281133	Nov 08, 2017 (151)
23	SWEGEN	ss3016467778	Nov 08, 2017 (151)
24	CSHL	ss3352006024	Nov 08, 2017 (151)
25	EGCUT_WGS	ss3683306349	Jul 13, 2019 (153)
26	EVA_DECODE	ss3701587300	Jul 13, 2019 (153)
27	ACPOP	ss3742511611	Jul 13, 2019 (153)
28	EVA	ss3755342498	Jul 13, 2019 (153)
29	KHV_HUMAN_GENOMES	ss3820607618	Jul 13, 2019 (153)
30	SGDP_PRJ	ss3886944759	Apr 27, 2020 (154)
31	KRGDB	ss3936806737	Apr 27, 2020 (154)
32	KOGIC	ss3980081360	Apr 27, 2020 (154)
33	TOPMED	ss5055421760	Apr 26, 2021 (155)
34	TOMMO_GENOMICS	ss5225009365	Apr 26, 2021 (155)
35	1000G_HIGH_COVERAGE	ss5305169158	Oct 16, 2022 (156)
36	EVA	ss5431190171	Oct 16, 2022 (156)
37	HUGCELL_USP	ss5497952470	Oct 16, 2022 (156)
38	EVA	ss5511924998	Oct 16, 2022 (156)
39	1000G_HIGH_COVERAGE	ss5609946054	Oct 16, 2022 (156)
40	SANFORD_IMAGENETICS	ss5661224968	Oct 16, 2022 (156)
41	TOMMO_GENOMICS	ss5782754443	Oct 16, 2022 (156)
42	YY_MCH	ss5817065312	Oct 16, 2022 (156)
43	EVA	ss5827493974	Oct 16, 2022 (156)
44	EVA	ss5852037618	Oct 16, 2022 (156)
45	EVA	ss5873936756	Oct 16, 2022 (156)
46	EVA	ss5952634282	Oct 16, 2022 (156)
47	1000Genomes	NC_000018.9 - 40337881	Oct 12, 2018 (152)
48	1000Genomes_30x	NC_000018.10 - 42757916	Oct 16, 2022 (156)
49	The Avon Longitudinal Study of Parents and Children	NC_000018.9 - 40337881	Oct 12, 2018 (152)
50	Genetic variation in the Estonian population	NC_000018.9 - 40337881	Oct 12, 2018 (152)
51	The Danish reference pan genome	NC_000018.9 - 40337881	Apr 27, 2020 (154)
52	gnomAD - Genomes	NC_000018.10 - 42757916	Apr 26, 2021 (155)
53	Genome of the Netherlands Release 5	NC_000018.9 - 40337881	Apr 27, 2020 (154)
54	KOREAN population from KRGDB	NC_000018.9 - 40337881	Apr 27, 2020 (154)
55	Korean Genome Project	NC_000018.10 - 42757916	Apr 27, 2020 (154)
56	Northern Sweden	NC_000018.9 - 40337881	Jul 13, 2019 (153)
57	Qatari	NC_000018.9 - 40337881	Apr 27, 2020 (154)
58	SGDP_PRJ	NC_000018.9 - 40337881	Apr 27, 2020 (154)
59	Siberian	NC_000018.9 - 40337881	Apr 27, 2020 (154)
60	8.3KJPN	NC_000018.9 - 40337881	Apr 26, 2021 (155)
61	14KJPN	NC_000018.10 - 42757916	Oct 16, 2022 (156)
62	TopMed	NC_000018.10 - 42757916	Apr 26, 2021 (155)
63	UK 10K study - Twins	NC_000018.9 - 40337881	Oct 12, 2018 (152)
64	A Vietnamese Genetic Variation Database	NC_000018.9 - 40337881	Jul 13, 2019 (153)
65	ALFA	NC_000018.10 - 42757916	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
ss168127089, ss282975939, ss287276440, ss1697745251	NC_000018.8:38591878:T:A	NC_000018.10:42757915:T:A	(self)
74204745, 41108846, 29044597, 4579930, 18317121, 43984131, 15796476, 19199382, 38961739, 10368777, 82978672, 41108846, 9083475, ss237450550, ss243703193, ss661448048, ss993688730, ss1081471623, ss1360880347, ss1578387226, ss1636792825, ss1679786858, ss1937157460, ss1968514805, ss2029347991, ss2157852423, ss2629172183, ss2702438401, ss2956281133, ss3016467778, ss3352006024, ss3683306349, ss3742511611, ss3755342498, ss3886944759, ss3936806737, ss5225009365, ss5431190171, ss5511924998, ss5661224968, ss5827493974, ss5952634282	NC_000018.9:40337880:T:A	NC_000018.10:42757915:T:A	(self)
97471989, 523497878, 36459361, 116591547, 270967423, 6583930203, ss2221270455, ss3701587300, ss3820607618, ss3980081360, ss5055421760, ss5305169158, ss5497952470, ss5609946054, ss5782754443, ss5817065312, ss5852037618, ss5873936756	NC_000018.10:42757915:T:A	NC_000018.10:42757915:T:A	(self)
ss155096778	NT_010966.14:21826982:T:A	NC_000018.10:42757915:T:A	(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 rs75164237

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

rs75164237