Name: rs9362544
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.

rs9362544

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:88716094 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.118675 (31412/264690, TOPMED)
G=0.116122 (16187/139396, GnomAD)
G=0.10815 (3056/28258, 14KJPN) (+ 9 more)
G=0.10835 (1816/16760, 8.3KJPN)
G=0.11432 (1867/16332, ALFA)
G=0.1135 (727/6404, 1000G_30x)
G=0.0856 (250/2922, KOREAN)
G=0.140 (140/998, GoNL)
G=0.143 (86/600, NorthernSweden)
G=0.255 (55/216, Qatari)
T=0.47 (43/92, SGDP_PRJ)
G=0.17 (7/40, GENOME_DK)

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	16332	T=0.88568	G=0.11432
European	Sub	12080	T=0.88626	G=0.11374
African	Sub	2816	T=0.8757	G=0.1243
African Others	Sub	108	T=0.917	G=0.083
African American	Sub	2708	T=0.8741	G=0.1259
Asian	Sub	108	T=0.917	G=0.083
East Asian	Sub	84	T=0.92	G=0.08
Other Asian	Sub	24	T=0.92	G=0.08
Latin American 1	Sub	146	T=0.822	G=0.178
Latin American 2	Sub	610	T=0.939	G=0.061
South Asian	Sub	94	T=0.81	G=0.19
Other	Sub	478	T=0.889	G=0.111

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=0.881325	G=0.118675
gnomAD - Genomes	Global	Study-wide	139396	T=0.883878	G=0.116122
gnomAD - Genomes	European	Sub	75796	T=0.88568	G=0.11432
gnomAD - Genomes	African	Sub	41402	T=0.87790	G=0.12210
gnomAD - Genomes	American	Sub	13614	T=0.90172	G=0.09828
gnomAD - Genomes	Ashkenazi Jewish	Sub	3314	T=0.8021	G=0.1979
gnomAD - Genomes	East Asian	Sub	3132	T=0.9345	G=0.0655
gnomAD - Genomes	Other	Sub	2138	T=0.8746	G=0.1254
14KJPN	JAPANESE	Study-wide	28258	T=0.89185	G=0.10815
8.3KJPN	JAPANESE	Study-wide	16760	T=0.89165	G=0.10835
Allele Frequency Aggregator	Total	Global	16332	T=0.88568	G=0.11432
Allele Frequency Aggregator	European	Sub	12080	T=0.88626	G=0.11374
Allele Frequency Aggregator	African	Sub	2816	T=0.8757	G=0.1243
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.939	G=0.061
Allele Frequency Aggregator	Other	Sub	478	T=0.889	G=0.111
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.822	G=0.178
Allele Frequency Aggregator	Asian	Sub	108	T=0.917	G=0.083
Allele Frequency Aggregator	South Asian	Sub	94	T=0.81	G=0.19
1000Genomes_30x	Global	Study-wide	6404	T=0.8865	G=0.1135
1000Genomes_30x	African	Sub	1786	T=0.8942	G=0.1058
1000Genomes_30x	Europe	Sub	1266	T=0.8863	G=0.1137
1000Genomes_30x	South Asian	Sub	1202	T=0.8062	G=0.1938
1000Genomes_30x	East Asian	Sub	1170	T=0.9222	G=0.0778
1000Genomes_30x	American	Sub	980	T=0.929	G=0.071
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.9144	G=0.0856
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.860	G=0.140
Northern Sweden	ACPOP	Study-wide	600	T=0.857	G=0.143
Qatari	Global	Study-wide	216	T=0.745	G=0.255
SGDP_PRJ	Global	Study-wide	92	T=0.47	G=0.53
The Danish reference pan genome	Danish	Study-wide	40	T=0.82	G=0.17

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.88716094T>G
GRCh37.p13 chr 6	NC_000006.11:g.89425813T>G

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.1371-376… NM_001286426.2:c.1371-37675A>C	N/A	Intron Variant
RNGTT transcript variant 3	NM_001286428.2:c.1191-376… NM_001286428.2:c.1191-37675A>C	N/A	Intron Variant
RNGTT transcript variant 1	NM_003800.5:c.1440-37675A… NM_003800.5:c.1440-37675A>C	N/A	Intron Variant
RNGTT transcript variant X1	XM_047419442.1:c.1440-376… XM_047419442.1:c.1440-37675A>C	N/A	Intron Variant
RNGTT transcript variant X2	XM_047419443.1:c.1440-376… XM_047419443.1:c.1440-37675A>C	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=	G
GRCh38.p14 chr 6	NC_000006.12:g.88716094=	NC_000006.12:g.88716094T>G
GRCh37.p13 chr 6	NC_000006.11:g.89425813=	NC_000006.11:g.89425813T>G
RNGTT transcript variant 2	NM_001286426.2:c.1371-37675=	NM_001286426.2:c.1371-37675A>C
RNGTT transcript variant 3	NM_001286428.2:c.1191-37675=	NM_001286428.2:c.1191-37675A>C
RNGTT transcript	NM_003800.3:c.1440-37675=	NM_003800.3:c.1440-37675A>C
RNGTT transcript variant 1	NM_003800.5:c.1440-37675=	NM_003800.5:c.1440-37675A>C
RNGTT transcript variant X1	XM_005248767.1:c.1371-37675=	XM_005248767.1:c.1371-37675A>C
RNGTT transcript variant X1	XM_047419442.1:c.1440-37675=	XM_047419442.1:c.1440-37675A>C
RNGTT transcript variant X2	XM_047419443.1:c.1440-37675=	XM_047419443.1:c.1440-37675A>C

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#.

28 SubSNP, 12 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss12824783	Dec 05, 2003 (119)
2	ABI	ss42860592	Mar 16, 2006 (126)
3	GMI	ss278913472	May 04, 2012 (137)
4	EVA-GONL	ss983211392	Aug 21, 2014 (142)
5	EVA_GENOME_DK	ss1581784162	Apr 01, 2015 (144)
6	WEILL_CORNELL_DGM	ss1926469101	Feb 12, 2016 (147)
7	GRF	ss2707688700	Nov 08, 2017 (151)
8	GNOMAD	ss2841969356	Nov 08, 2017 (151)
9	SWEGEN	ss2999510960	Nov 08, 2017 (151)
10	CSHL	ss3347103392	Nov 08, 2017 (151)
11	URBANLAB	ss3648412587	Oct 12, 2018 (152)
12	ACPOP	ss3733741753	Jul 13, 2019 (153)
13	PACBIO	ss3785547601	Jul 13, 2019 (153)
14	PACBIO	ss3790887623	Jul 13, 2019 (153)
15	PACBIO	ss3795766781	Jul 13, 2019 (153)
16	EVA	ss3838511429	Apr 26, 2020 (154)
17	EVA	ss3843959380	Apr 26, 2020 (154)
18	SGDP_PRJ	ss3865136258	Apr 26, 2020 (154)
19	KRGDB	ss3912029974	Apr 26, 2020 (154)
20	TOPMED	ss4712156446	Apr 26, 2021 (155)
21	TOMMO_GENOMICS	ss5178690915	Apr 26, 2021 (155)
22	1000G_HIGH_COVERAGE	ss5269382446	Oct 14, 2022 (156)
23	EVA	ss5367269083	Oct 14, 2022 (156)
24	1000G_HIGH_COVERAGE	ss5555802529	Oct 14, 2022 (156)
25	SANFORD_IMAGENETICS	ss5640941754	Oct 14, 2022 (156)
26	TOMMO_GENOMICS	ss5717212214	Oct 14, 2022 (156)
27	YY_MCH	ss5807715285	Oct 14, 2022 (156)
28	EVA	ss5842618168	Oct 14, 2022 (156)
29	1000Genomes_30x	NC_000006.12 - 88716094	Oct 14, 2022 (156)
30	The Danish reference pan genome	NC_000006.11 - 89425813	Apr 26, 2020 (154)
31	gnomAD - Genomes	NC_000006.12 - 88716094	Apr 26, 2021 (155)
32	Genome of the Netherlands Release 5	NC_000006.11 - 89425813	Apr 26, 2020 (154)
33	KOREAN population from KRGDB	NC_000006.11 - 89425813	Apr 26, 2020 (154)
34	Northern Sweden	NC_000006.11 - 89425813	Jul 13, 2019 (153)
35	Qatari	NC_000006.11 - 89425813	Apr 26, 2020 (154)
36	SGDP_PRJ	NC_000006.11 - 89425813	Apr 26, 2020 (154)
37	8.3KJPN	NC_000006.11 - 89425813	Apr 26, 2021 (155)
38	14KJPN	NC_000006.12 - 88716094	Oct 14, 2022 (156)
39	TopMed	NC_000006.12 - 88716094	Apr 26, 2021 (155)
40	ALFA	NC_000006.12 - 88716094	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)
rs36157183	Oct 15, 2006 (127)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss278913472	NC_000006.10:89482531:T:G	NC_000006.12:88716093:T:G	(self)
7949101, 8193008, 19207368, 7026618, 8511031, 17153238, 36660222, ss983211392, ss1581784162, ss1926469101, ss2707688700, ss2841969356, ss2999510960, ss3347103392, ss3733741753, ss3785547601, ss3790887623, ss3795766781, ss3838511429, ss3865136258, ss3912029974, ss5178690915, ss5367269083, ss5640941754, ss5842618168	NC_000006.11:89425812:T:G	NC_000006.12:88716093:T:G	(self)
43328464, 232950890, 51049318, 549534004, 3354979754, ss3648412587, ss3843959380, ss4712156446, ss5269382446, ss5555802529, ss5717212214, ss5807715285	NC_000006.12:88716093:T:G	NC_000006.12:88716093:T:G	(self)
ss12824783	NT_007299.12:27245983:T:G	NC_000006.12:88716093:T:G	(self)
ss42860592	NT_007299.13:27545646:T:G	NC_000006.12:88716093:T:G	(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 rs9362544

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

rs9362544