Name: rs35166568
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.

rs35166568

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:88945990 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.011428 (3025/264690, TOPMED)
C=0.011185 (1569/140282, GnomAD)
C=0.01329 (255/19188, ALFA) (+ 10 more)
C=0.0047 (30/6404, 1000G_30x)
C=0.0050 (25/5008, 1000G)
C=0.0056 (25/4480, Estonian)
C=0.0202 (78/3854, ALSPAC)
C=0.0200 (74/3708, TWINSUK)
C=0.014 (14/998, GoNL)
C=0.017 (10/600, NorthernSweden)
C=0.014 (3/216, Qatari)
T=0.5 (2/4, SGDP_PRJ)
C=0.5 (2/4, SGDP_PRJ)

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	19188	T=0.98671	C=0.01329
European	Sub	14286	T=0.98404	C=0.01596
African	Sub	2970	T=0.9956	C=0.0044
African Others	Sub	114	T=1.000	C=0.000
African American	Sub	2856	T=0.9954	C=0.0046
Asian	Sub	116	T=1.000	C=0.000
East Asian	Sub	88	T=1.00	C=0.00
Other Asian	Sub	28	T=1.00	C=0.00
Latin American 1	Sub	154	T=0.974	C=0.026
Latin American 2	Sub	616	T=0.995	C=0.005
South Asian	Sub	98	T=0.99	C=0.01
Other	Sub	948	T=0.994	C=0.006

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=0.988572	C=0.011428
gnomAD - Genomes	Global	Study-wide	140282	T=0.988815	C=0.011185
gnomAD - Genomes	European	Sub	75956	T=0.98398	C=0.01602
gnomAD - Genomes	African	Sub	42058	T=0.99593	C=0.00407
gnomAD - Genomes	American	Sub	13660	T=0.99100	C=0.00900
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.9880	C=0.0120
gnomAD - Genomes	East Asian	Sub	3130	T=1.0000	C=0.0000
gnomAD - Genomes	Other	Sub	2154	T=0.9916	C=0.0084
Allele Frequency Aggregator	Total	Global	19188	T=0.98671	C=0.01329
Allele Frequency Aggregator	European	Sub	14286	T=0.98404	C=0.01596
Allele Frequency Aggregator	African	Sub	2970	T=0.9956	C=0.0044
Allele Frequency Aggregator	Other	Sub	948	T=0.994	C=0.006
Allele Frequency Aggregator	Latin American 2	Sub	616	T=0.995	C=0.005
Allele Frequency Aggregator	Latin American 1	Sub	154	T=0.974	C=0.026
Allele Frequency Aggregator	Asian	Sub	116	T=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=0.99	C=0.01
1000Genomes_30x	Global	Study-wide	6404	T=0.9953	C=0.0047
1000Genomes_30x	African	Sub	1786	T=0.9989	C=0.0011
1000Genomes_30x	Europe	Sub	1266	T=0.9866	C=0.0134
1000Genomes_30x	South Asian	Sub	1202	T=0.9925	C=0.0075
1000Genomes_30x	East Asian	Sub	1170	T=1.0000	C=0.0000
1000Genomes_30x	American	Sub	980	T=0.998	C=0.002
1000Genomes	Global	Study-wide	5008	T=0.9950	C=0.0050
1000Genomes	African	Sub	1322	T=0.9985	C=0.0015
1000Genomes	East Asian	Sub	1008	T=1.0000	C=0.0000
1000Genomes	Europe	Sub	1006	T=0.9861	C=0.0139
1000Genomes	South Asian	Sub	978	T=0.993	C=0.007
1000Genomes	American	Sub	694	T=0.997	C=0.003
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9944	C=0.0056
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9798	C=0.0202
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9800	C=0.0200
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.986	C=0.014
Northern Sweden	ACPOP	Study-wide	600	T=0.983	C=0.017
Qatari	Global	Study-wide	216	T=0.986	C=0.014
SGDP_PRJ	Global	Study-wide	4	T=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.88945990T>C
GRCh37.p13 chr 6	NC_000006.11:g.89655709T>C

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.65-4810A… NM_001286426.2:c.65-4810A>G	N/A	Intron Variant
RNGTT transcript variant 3	NM_001286428.2:c.-6-16723… NM_001286428.2:c.-6-16723A>G	N/A	Intron Variant
RNGTT transcript variant 1	NM_003800.5:c.65-4810A>G	N/A	Intron Variant
RNGTT transcript variant X1	XM_047419442.1:c.65-4810A… XM_047419442.1:c.65-4810A>G	N/A	Intron Variant
RNGTT transcript variant X2	XM_047419443.1:c.65-4810A… XM_047419443.1:c.65-4810A>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	T=	C
GRCh38.p14 chr 6	NC_000006.12:g.88945990=	NC_000006.12:g.88945990T>C
GRCh37.p13 chr 6	NC_000006.11:g.89655709=	NC_000006.11:g.89655709T>C
RNGTT transcript variant 2	NM_001286426.2:c.65-4810=	NM_001286426.2:c.65-4810A>G
RNGTT transcript variant 3	NM_001286428.2:c.-6-16723=	NM_001286428.2:c.-6-16723A>G
RNGTT transcript	NM_003800.3:c.65-4810=	NM_003800.3:c.65-4810A>G
RNGTT transcript variant 1	NM_003800.5:c.65-4810=	NM_003800.5:c.65-4810A>G
RNGTT transcript variant X1	XM_005248767.1:c.65-4810=	XM_005248767.1:c.65-4810A>G
RNGTT transcript variant X1	XM_047419442.1:c.65-4810=	XM_047419442.1:c.65-4810A>G
RNGTT transcript variant X2	XM_047419443.1:c.65-4810=	XM_047419443.1:c.65-4810A>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#.

34 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	ABI	ss44689032	Mar 14, 2006 (126)
2	HUMANGENOME_JCVI	ss98518930	Feb 06, 2009 (130)
3	ENSEMBL	ss139317134	Dec 01, 2009 (131)
4	1000GENOMES	ss233577601	Jul 15, 2010 (132)
5	ILLUMINA	ss534687222	Sep 08, 2015 (146)
6	EVA-GONL	ss983212910	Aug 21, 2014 (142)
7	1000GENOMES	ss1321189910	Aug 21, 2014 (142)
8	EVA_DECODE	ss1592765271	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1616115673	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1659109706	Apr 01, 2015 (144)
11	WEILL_CORNELL_DGM	ss1926470418	Feb 12, 2016 (147)
12	JJLAB	ss2023878446	Sep 14, 2016 (149)
13	HUMAN_LONGEVITY	ss2286062302	Dec 20, 2016 (150)
14	GNOMAD	ss2841986055	Nov 08, 2017 (151)
15	SWEGEN	ss2999513061	Nov 08, 2017 (151)
16	ILLUMINA	ss3629598479	Oct 12, 2018 (152)
17	URBANLAB	ss3648412965	Oct 12, 2018 (152)
18	EGCUT_WGS	ss3667394563	Jul 13, 2019 (153)
19	EVA_DECODE	ss3717734455	Jul 13, 2019 (153)
20	ACPOP	ss3733742825	Jul 13, 2019 (153)
21	SGDP_PRJ	ss3865139108	Apr 26, 2020 (154)
22	TOPMED	ss4712208038	Apr 26, 2021 (155)
23	1000G_HIGH_COVERAGE	ss5269387463	Oct 14, 2022 (156)
24	EVA	ss5367277684	Oct 14, 2022 (156)
25	HUGCELL_USP	ss5466922300	Oct 14, 2022 (156)
26	EVA	ss5508608755	Oct 14, 2022 (156)
27	1000G_HIGH_COVERAGE	ss5555810037	Oct 14, 2022 (156)
28	SANFORD_IMAGENETICS	ss5624635457	Oct 14, 2022 (156)
29	SANFORD_IMAGENETICS	ss5640944588	Oct 14, 2022 (156)
30	EVA	ss5842619994	Oct 14, 2022 (156)
31	EVA	ss5848105061	Oct 14, 2022 (156)
32	EVA	ss5884854562	Oct 14, 2022 (156)
33	EVA	ss5969448226	Oct 14, 2022 (156)
34	EVA	ss5979794289	Oct 14, 2022 (156)
35	1000Genomes	NC_000006.11 - 89655709	Oct 12, 2018 (152)
36	1000Genomes_30x	NC_000006.12 - 88945990	Oct 14, 2022 (156)
37	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 89655709	Oct 12, 2018 (152)
38	Genetic variation in the Estonian population	NC_000006.11 - 89655709	Oct 12, 2018 (152)
39	gnomAD - Genomes	NC_000006.12 - 88945990	Apr 26, 2021 (155)
40	Genome of the Netherlands Release 5	NC_000006.11 - 89655709	Apr 26, 2020 (154)
41	Northern Sweden	NC_000006.11 - 89655709	Jul 13, 2019 (153)
42	Qatari	NC_000006.11 - 89655709	Apr 26, 2020 (154)
43	SGDP_PRJ	NC_000006.11 - 89655709	Apr 26, 2020 (154)
44	TopMed	NC_000006.12 - 88945990	Apr 26, 2021 (155)
45	UK 10K study - Twins	NC_000006.11 - 89655709	Oct 12, 2018 (152)
46	ALFA	NC_000006.12 - 88945990	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
ss1592765271	NC_000006.10:89712427:T:C	NC_000006.12:88945989:T:C	(self)
33017100, 18388618, 13132811, 8194501, 7027690, 8512348, 17156088, 18388618, ss233577601, ss534687222, ss983212910, ss1321189910, ss1616115673, ss1659109706, ss1926470418, ss2023878446, ss2841986055, ss2999513061, ss3629598479, ss3667394563, ss3733742825, ss3865139108, ss5367277684, ss5508608755, ss5624635457, ss5640944588, ss5842619994, ss5848105061, ss5969448226, ss5979794289	NC_000006.11:89655708:T:C	NC_000006.12:88945989:T:C	(self)
43335972, 232994372, 549585596, 8710953319, ss2286062302, ss3648412965, ss3717734455, ss4712208038, ss5269387463, ss5466922300, ss5555810037, ss5884854562	NC_000006.12:88945989:T:C	NC_000006.12:88945989:T:C	(self)
ss44689032, ss98518930, ss139317134	NT_007299.13:27775542:T:C	NC_000006.12:88945989: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 rs35166568

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

rs35166568