Name: rs12195358
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.

rs12195358

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:88929938 (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 / A>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.046133 (12211/264690, TOPMED)
C=0.046465 (6406/137868, GnomAD)
C=0.01528 (277/18132, ALFA) (+ 13 more)
C=0.0567 (284/5008, 1000G)
C=0.0169 (65/3854, ALSPAC)
C=0.0197 (73/3708, TWINSUK)
C=0.0993 (291/2930, KOREAN)
C=0.0846 (155/1832, Korea1K)
C=0.017 (17/998, GoNL)
C=0.013 (8/600, NorthernSweden)
C=0.056 (12/216, Qatari)
C=0.061 (13/212, Vietnamese)
A=0.402 (45/112, SGDP_PRJ)
C=0.05 (2/40, GENOME_DK)
A=0.5 (2/4, Siberian)
C=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: RNGTT : 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	18132	A=0.98472	C=0.01528, T=0.00000
European	Sub	13966	A=0.98539	C=0.01461, T=0.00000
African	Sub	2614	A=0.9755	C=0.0245, T=0.0000
African Others	Sub	94	A=0.97	C=0.03, T=0.00
African American	Sub	2520	A=0.9758	C=0.0242, T=0.0000
Asian	Sub	100	A=0.99	C=0.01, T=0.00
East Asian	Sub	78	A=0.99	C=0.01, T=0.00
Other Asian	Sub	22	A=1.00	C=0.00, T=0.00
Latin American 1	Sub	134	A=1.000	C=0.000, T=0.000
Latin American 2	Sub	580	A=1.000	C=0.000, T=0.000
South Asian	Sub	92	A=1.00	C=0.00, T=0.00
Other	Sub	646	A=0.988	C=0.012, T=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
TopMed	Global	Study-wide	264690	A=0.953867	C=0.046133
gnomAD - Genomes	Global	Study-wide	137868	A=0.953535	C=0.046465
gnomAD - Genomes	European	Sub	74910	A=0.97282	C=0.02718
gnomAD - Genomes	African	Sub	41028	A=0.91637	C=0.08363
gnomAD - Genomes	American	Sub	13390	A=0.96393	C=0.03607
gnomAD - Genomes	Ashkenazi Jewish	Sub	3310	A=0.9846	C=0.0154
gnomAD - Genomes	East Asian	Sub	3112	A=0.8969	C=0.1031
gnomAD - Genomes	Other	Sub	2118	A=0.9603	C=0.0397
Allele Frequency Aggregator	Total	Global	18132	A=0.98472	C=0.01528, T=0.00000
Allele Frequency Aggregator	European	Sub	13966	A=0.98539	C=0.01461, T=0.00000
Allele Frequency Aggregator	African	Sub	2614	A=0.9755	C=0.0245, T=0.0000
Allele Frequency Aggregator	Other	Sub	646	A=0.988	C=0.012, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	580	A=1.000	C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	134	A=1.000	C=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	100	A=0.99	C=0.01, T=0.00
Allele Frequency Aggregator	South Asian	Sub	92	A=1.00	C=0.00, T=0.00
1000Genomes	Global	Study-wide	5008	A=0.9433	C=0.0567
1000Genomes	African	Sub	1322	A=0.9145	C=0.0855
1000Genomes	East Asian	Sub	1008	A=0.9177	C=0.0823
1000Genomes	Europe	Sub	1006	A=0.9702	C=0.0298
1000Genomes	South Asian	Sub	978	A=0.963	C=0.037
1000Genomes	American	Sub	694	A=0.968	C=0.032
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.9831	C=0.0169
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9803	C=0.0197
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.9003	C=0.0993, G=0.0003
Korean Genome Project	KOREAN	Study-wide	1832	A=0.9154	C=0.0846
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.983	C=0.017
Northern Sweden	ACPOP	Study-wide	600	A=0.987	C=0.013
Qatari	Global	Study-wide	216	A=0.944	C=0.056
A Vietnamese Genetic Variation Database	Global	Study-wide	212	A=0.939	C=0.061
SGDP_PRJ	Global	Study-wide	112	A=0.402	C=0.598
The Danish reference pan genome	Danish	Study-wide	40	A=0.95	C=0.05
Siberian	Global	Study-wide	4	A=0.5	C=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 6	NC_000006.12:g.88929938A>C
GRCh38.p14 chr 6	NC_000006.12:g.88929938A>G
GRCh38.p14 chr 6	NC_000006.12:g.88929938A>T
GRCh37.p13 chr 6	NC_000006.11:g.89639657A>C
GRCh37.p13 chr 6	NC_000006.11:g.89639657A>G
GRCh37.p13 chr 6	NC_000006.11:g.89639657A>T

Gene: RNGTT, RNA guanylyltransferase and 5'-phosphatase (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
RNGTT transcript variant 2	NM_001286426.2:c.175-671T… NM_001286426.2:c.175-671T>G	N/A	Intron Variant
RNGTT transcript variant 3	NM_001286428.2:c.-6-671T>G	N/A	Intron Variant
RNGTT transcript variant 1	NM_003800.5:c.175-671T>G	N/A	Intron Variant
RNGTT transcript variant X1	XM_047419442.1:c.175-671T… XM_047419442.1:c.175-671T>G	N/A	Intron Variant
RNGTT transcript variant X2	XM_047419443.1:c.175-671T… XM_047419443.1:c.175-671T>G	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	A=	C	G	T
GRCh38.p14 chr 6	NC_000006.12:g.88929938=	NC_000006.12:g.88929938A>C	NC_000006.12:g.88929938A>G	NC_000006.12:g.88929938A>T
GRCh37.p13 chr 6	NC_000006.11:g.89639657=	NC_000006.11:g.89639657A>C	NC_000006.11:g.89639657A>G	NC_000006.11:g.89639657A>T
RNGTT transcript variant 2	NM_001286426.2:c.175-671=	NM_001286426.2:c.175-671T>G	NM_001286426.2:c.175-671T>C	NM_001286426.2:c.175-671T>A
RNGTT transcript variant 3	NM_001286428.2:c.-6-671=	NM_001286428.2:c.-6-671T>G	NM_001286428.2:c.-6-671T>C	NM_001286428.2:c.-6-671T>A
RNGTT transcript	NM_003800.3:c.175-671=	NM_003800.3:c.175-671T>G	NM_003800.3:c.175-671T>C	NM_003800.3:c.175-671T>A
RNGTT transcript variant 1	NM_003800.5:c.175-671=	NM_003800.5:c.175-671T>G	NM_003800.5:c.175-671T>C	NM_003800.5:c.175-671T>A
RNGTT transcript variant X1	XM_005248767.1:c.175-671=	XM_005248767.1:c.175-671T>G	XM_005248767.1:c.175-671T>C	XM_005248767.1:c.175-671T>A
RNGTT transcript variant X1	XM_047419442.1:c.175-671=	XM_047419442.1:c.175-671T>G	XM_047419442.1:c.175-671T>C	XM_047419442.1:c.175-671T>A
RNGTT transcript variant X2	XM_047419443.1:c.175-671=	XM_047419443.1:c.175-671T>G	XM_047419443.1:c.175-671T>C	XM_047419443.1:c.175-671T>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#.

42 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss18375418	Feb 28, 2004 (120)
2	ILLUMINA-UK	ss116598223	Dec 01, 2009 (131)
3	1000GENOMES	ss222529590	Jul 14, 2010 (132)
4	1000GENOMES	ss233577578	Jul 15, 2010 (132)
5	1000GENOMES	ss240612946	Jul 15, 2010 (132)
6	GMI	ss278913941	May 04, 2012 (137)
7	SSMP	ss653354887	Apr 25, 2013 (138)
8	EVA-GONL	ss983212792	Aug 21, 2014 (142)
9	JMKIDD_LAB	ss1073817765	Aug 21, 2014 (142)
10	1000GENOMES	ss1321189461	Aug 21, 2014 (142)
11	EVA_GENOME_DK	ss1581784612	Apr 01, 2015 (144)
12	EVA_UK10K_ALSPAC	ss1616115410	Apr 01, 2015 (144)
13	EVA_UK10K_TWINSUK	ss1659109443	Apr 01, 2015 (144)
14	WEILL_CORNELL_DGM	ss1926470311	Feb 12, 2016 (147)
15	USC_VALOUEV	ss2152070342	Dec 20, 2016 (150)
16	HUMAN_LONGEVITY	ss2286061374	Dec 20, 2016 (150)
17	GRF	ss2707689345	Nov 08, 2017 (151)
18	GNOMAD	ss2841984869	Nov 08, 2017 (151)
19	SWEGEN	ss2999512902	Nov 08, 2017 (151)
20	EVA_DECODE	ss3717734237	Jul 13, 2019 (153)
21	ACPOP	ss3733742747	Jul 13, 2019 (153)
22	EVA	ss3765338386	Jul 13, 2019 (153)
23	KHV_HUMAN_GENOMES	ss3808489418	Jul 13, 2019 (153)
24	EVA	ss3830060983	Apr 26, 2020 (154)
25	SGDP_PRJ	ss3865138880	Apr 26, 2020 (154)
26	KRGDB	ss3912033022	Apr 26, 2020 (154)
27	KOGIC	ss3959551577	Apr 26, 2020 (154)
28	TOPMED	ss4712204335	Apr 26, 2021 (155)
29	TOMMO_GENOMICS	ss5178696833	Apr 26, 2021 (155)
30	TOMMO_GENOMICS	ss5178696834	Apr 26, 2021 (155)
31	1000G_HIGH_COVERAGE	ss5269387045	Oct 14, 2022 (156)
32	EVA	ss5367277054	Oct 14, 2022 (156)
33	HUGCELL_USP	ss5466921911	Oct 14, 2022 (156)
34	EVA	ss5508608738	Oct 14, 2022 (156)
35	SANFORD_IMAGENETICS	ss5640944361	Oct 14, 2022 (156)
36	TOMMO_GENOMICS	ss5717219763	Oct 14, 2022 (156)
37	TOMMO_GENOMICS	ss5717219765	Oct 14, 2022 (156)
38	YY_MCH	ss5807716316	Oct 14, 2022 (156)
39	EVA	ss5842619859	Oct 14, 2022 (156)
40	EVA	ss5855465361	Oct 14, 2022 (156)
41	EVA	ss5884854081	Oct 14, 2022 (156)
42	EVA	ss5969447967	Oct 14, 2022 (156)
43	1000Genomes	NC_000006.11 - 89639657	Oct 12, 2018 (152)
44	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 89639657	Oct 12, 2018 (152)
45	The Danish reference pan genome	NC_000006.11 - 89639657	Apr 26, 2020 (154)
46	gnomAD - Genomes	NC_000006.12 - 88929938	Apr 26, 2021 (155)
47	Genome of the Netherlands Release 5	NC_000006.11 - 89639657	Apr 26, 2020 (154)
48	KOREAN population from KRGDB	NC_000006.11 - 89639657	Apr 26, 2020 (154)
49	Korean Genome Project	NC_000006.12 - 88929938	Apr 26, 2020 (154)
50	Northern Sweden	NC_000006.11 - 89639657	Jul 13, 2019 (153)
51	Qatari	NC_000006.11 - 89639657	Apr 26, 2020 (154)
52	SGDP_PRJ	NC_000006.11 - 89639657	Apr 26, 2020 (154)
53	Siberian	NC_000006.11 - 89639657	Apr 26, 2020 (154)
54	8.3KJPN Submission ignored due to conflicting rows: Row 36666140 (NC_000006.11:89639656:A:C 1492/16758) Row 36666141 (NC_000006.11:89639656:A:G 1/16758)	-	Apr 26, 2021 (155)
55	8.3KJPN Submission ignored due to conflicting rows: Row 36666140 (NC_000006.11:89639656:A:C 1492/16758) Row 36666141 (NC_000006.11:89639656:A:G 1/16758)	-	Apr 26, 2021 (155)
56	14KJPN Submission ignored due to conflicting rows: Row 51056867 (NC_000006.12:88929937:A:C 2410/28246) Row 51056869 (NC_000006.12:88929937:A:G 1/28246)	-	Oct 14, 2022 (156)
57	14KJPN Submission ignored due to conflicting rows: Row 51056867 (NC_000006.12:88929937:A:C 2410/28246) Row 51056869 (NC_000006.12:88929937:A:G 1/28246)	-	Oct 14, 2022 (156)
58	TopMed	NC_000006.12 - 88929938	Apr 26, 2021 (155)
59	UK 10K study - Twins	NC_000006.11 - 89639657	Oct 12, 2018 (152)
60	A Vietnamese Genetic Variation Database	NC_000006.11 - 89639657	Jul 13, 2019 (153)
61	ALFA	NC_000006.12 - 88929938	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
ss116598223, ss278913941	NC_000006.10:89696375:A:C	NC_000006.12:88929937:A:C	(self)
33016633, 18388337, 7949551, 8194384, 19210416, 7027612, 8512241, 17155860, 4586696, 18388337, 4087404, ss222529590, ss233577578, ss240612946, ss653354887, ss983212792, ss1073817765, ss1321189461, ss1581784612, ss1616115410, ss1659109443, ss1926470311, ss2152070342, ss2707689345, ss2841984869, ss2999512902, ss3733742747, ss3765338386, ss3830060983, ss3865138880, ss3912033022, ss5178696833, ss5367277054, ss5508608738, ss5640944361, ss5842619859, ss5969447967	NC_000006.11:89639656:A:C	NC_000006.12:88929937:A:C	(self)
232991242, 15929578, 549581893, 2404695094, ss2286061374, ss3717734237, ss3808489418, ss3959551577, ss4712204335, ss5269387045, ss5466921911, ss5717219763, ss5807716316, ss5855465361, ss5884854081	NC_000006.12:88929937:A:C	NC_000006.12:88929937:A:C	(self)
ss18375418	NT_007299.12:27459827:A:C	NC_000006.12:88929937:A:C	(self)
19210416, ss3912033022, ss5178696834	NC_000006.11:89639656:A:G	NC_000006.12:88929937:A:G	(self)
ss5717219765	NC_000006.12:88929937:A:G	NC_000006.12:88929937:A:G
2404695094	NC_000006.12:88929937:A:T	NC_000006.12:88929937:A: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 rs12195358

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

rs12195358