Name: rs5946234
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.

rs5946234

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:114919629 (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: G>A
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.208984 (55316/264690, TOPMED)
G=0.02803 (623/22223, 14KJPN)
G=0.17684 (3275/18520, ALFA) (+ 12 more)
G=0.02920 (375/12843, 8.3KJPN)
G=0.1796 (863/4805, 1000G_30x)
G=0.1722 (650/3775, 1000G)
G=0.1583 (587/3708, TWINSUK)
G=0.0102 (30/2930, KOREAN)
G=0.1554 (449/2889, ALSPAC)
G=0.035 (17/490, SGDP_PRJ)
G=0.235 (77/328, HapMap)
G=0.185 (20/108, Qatari)
G=0.02 (1/54, Siberian)
G=0.02 (1/48, Vietnamese)
G=0.15 (6/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: None
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	18520	G=0.17684	A=0.82316
European	Sub	14152	G=0.14062	A=0.85938
African	Sub	2898	G=0.3765	A=0.6235
African Others	Sub	114	G=0.351	A=0.649
African American	Sub	2784	G=0.3775	A=0.6225
Asian	Sub	112	G=0.000	A=1.000
East Asian	Sub	86	G=0.00	A=1.00
Other Asian	Sub	26	G=0.00	A=1.00
Latin American 1	Sub	146	G=0.171	A=0.829
Latin American 2	Sub	610	G=0.067	A=0.933
South Asian	Sub	98	G=0.11	A=0.89
Other	Sub	504	G=0.232	A=0.768

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	G=0.208984	A=0.791016
14KJPN	JAPANESE	Study-wide	22223	G=0.02803	A=0.97197
Allele Frequency Aggregator	Total	Global	18520	G=0.17684	A=0.82316
Allele Frequency Aggregator	European	Sub	14152	G=0.14062	A=0.85938
Allele Frequency Aggregator	African	Sub	2898	G=0.3765	A=0.6235
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.067	A=0.933
Allele Frequency Aggregator	Other	Sub	504	G=0.232	A=0.768
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.171	A=0.829
Allele Frequency Aggregator	Asian	Sub	112	G=0.000	A=1.000
Allele Frequency Aggregator	South Asian	Sub	98	G=0.11	A=0.89
8.3KJPN	JAPANESE	Study-wide	12843	G=0.02920	A=0.97080
1000Genomes_30x	Global	Study-wide	4805	G=0.1796	A=0.8204
1000Genomes_30x	African	Sub	1328	G=0.4285	A=0.5715
1000Genomes_30x	Europe	Sub	961	G=0.149	A=0.851
1000Genomes_30x	South Asian	Sub	883	G=0.084	A=0.916
1000Genomes_30x	East Asian	Sub	878	G=0.011	A=0.989
1000Genomes_30x	American	Sub	755	G=0.089	A=0.911
1000Genomes	Global	Study-wide	3775	G=0.1722	A=0.8278
1000Genomes	African	Sub	1003	G=0.4207	A=0.5793
1000Genomes	Europe	Sub	766	G=0.150	A=0.850
1000Genomes	East Asian	Sub	764	G=0.013	A=0.987
1000Genomes	South Asian	Sub	718	G=0.078	A=0.922
1000Genomes	American	Sub	524	G=0.090	A=0.910
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.1583	A=0.8417
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.0102	A=0.9898
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	2889	G=0.1554	A=0.8446
SGDP_PRJ	Global	Study-wide	490	G=0.035	A=0.965
HapMap	Global	Study-wide	328	G=0.235	A=0.765
HapMap	African	Sub	120	G=0.475	A=0.525
HapMap	American	Sub	120	G=0.142	A=0.858
HapMap	Asian	Sub	88	G=0.03	A=0.97
Qatari	Global	Study-wide	108	G=0.185	A=0.815
Siberian	Global	Study-wide	54	G=0.02	A=0.98
A Vietnamese Genetic Variation Database	Global	Study-wide	48	G=0.02	A=0.98
The Danish reference pan genome	Danish	Study-wide	40	G=0.15	A=0.85

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 X	NC_000023.11:g.114919629G>A
GRCh37.p13 chr X fix patch HG1462_PATCH	NW_004070891.1:g.588431G>A
GRCh37.p13 chr X	NC_000023.10:g.114154192G>A

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	G=	A
GRCh38.p14 chr X	NC_000023.11:g.114919629=	NC_000023.11:g.114919629G>A
GRCh37.p13 chr X fix patch HG1462_PATCH	NW_004070891.1:g.588431=	NW_004070891.1:g.588431G>A
GRCh37.p13 chr X	NC_000023.10:g.114154192=	NC_000023.10:g.114154192G>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#.

55 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8230461	Apr 21, 2003 (114)
2	SC_SNP	ss8547110	Jul 11, 2003 (117)
3	WI_SSAHASNP	ss12051549	Jul 11, 2003 (117)
4	CSHL-HAPMAP	ss19812810	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss20388795	Feb 27, 2004 (120)
6	SSAHASNP	ss21044034	Apr 05, 2004 (121)
7	HGSV	ss78631637	Dec 07, 2007 (129)
8	KRIBB_YJKIM	ss80746962	Dec 15, 2007 (130)
9	HGSV	ss83939138	Dec 15, 2007 (130)
10	BGI	ss105757647	Feb 05, 2009 (130)
11	1000GENOMES	ss113001447	Jan 25, 2009 (130)
12	ILLUMINA-UK	ss115645293	Feb 14, 2009 (130)
13	ENSEMBL	ss133681590	Dec 01, 2009 (131)
14	GMI	ss157668105	Dec 01, 2009 (131)
15	BUSHMAN	ss204345994	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss208887150	Jul 04, 2010 (132)
17	BL	ss256106590	May 09, 2011 (134)
18	GMI	ss283843924	May 04, 2012 (137)
19	GMI	ss287639428	Apr 25, 2013 (138)
20	PJP	ss294494350	May 09, 2011 (134)
21	1000GENOMES	ss341732140	May 09, 2011 (134)
22	SSMP	ss662977363	Apr 25, 2013 (138)
23	JMKIDD_LAB	ss1083085027	Apr 09, 2015 (144)
24	DDI	ss1432103380	Apr 09, 2015 (144)
25	1000GENOMES	ss1555824276	Apr 09, 2015 (144)
26	EVA_GENOME_DK	ss1583482304	Apr 09, 2015 (144)
27	EVA_UK10K_ALSPAC	ss1641376073	Apr 09, 2015 (144)
28	EVA_UK10K_TWINSUK	ss1684370106	Apr 09, 2015 (144)
29	WEILL_CORNELL_DGM	ss1939644960	Feb 17, 2016 (147)
30	GENOMED	ss1971421849	Sep 28, 2016 (149)
31	USC_VALOUEV	ss2159199772	Oct 12, 2018 (152)
32	HUMAN_LONGEVITY	ss2319737580	Dec 20, 2016 (150)
33	SYSTEMSBIOZJU	ss2629759283	Oct 12, 2018 (152)
34	GRF	ss2710319427	Oct 12, 2018 (152)
35	GNOMAD	ss2982533132	Oct 12, 2018 (152)
36	SWEGEN	ss3020493219	Oct 12, 2018 (152)
37	BIOINF_KMB_FNS_UNIBA	ss3029100850	Nov 08, 2017 (151)
38	URBANLAB	ss3651320304	Oct 12, 2018 (152)
39	EVA	ss3770528879	Jul 14, 2019 (153)
40	KHV_HUMAN_GENOMES	ss3823309253	Jul 14, 2019 (153)
41	EVA	ss3836281983	Apr 27, 2020 (154)
42	EVA	ss3841745340	Apr 27, 2020 (154)
43	EVA	ss3847278504	Apr 27, 2020 (154)
44	SGDP_PRJ	ss3892095711	Apr 27, 2020 (154)
45	KRGDB	ss3942760933	Apr 27, 2020 (154)
46	TOPMED	ss5134676089	Apr 26, 2021 (155)
47	TOMMO_GENOMICS	ss5235934800	Apr 26, 2021 (155)
48	1000G_HIGH_COVERAGE	ss5313654022	Oct 17, 2022 (156)
49	HUGCELL_USP	ss5505098362	Oct 17, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5622594828	Oct 17, 2022 (156)
51	SANFORD_IMAGENETICS	ss5665751798	Oct 17, 2022 (156)
52	TOMMO_GENOMICS	ss5798211531	Oct 17, 2022 (156)
53	YY_MCH	ss5819292948	Oct 17, 2022 (156)
54	EVA	ss5857172738	Oct 17, 2022 (156)
55	EVA	ss5978848461	Oct 17, 2022 (156)
56	1000Genomes	NC_000023.10 - 114154192	Oct 12, 2018 (152)
57	1000Genomes_30x	NC_000023.11 - 114919629	Oct 17, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000023.10 - 114154192	Oct 12, 2018 (152)
59	The Danish reference pan genome	NC_000023.10 - 114154192	Apr 27, 2020 (154)
60	HapMap	NC_000023.11 - 114919629	Apr 27, 2020 (154)
61	KOREAN population from KRGDB	NC_000023.10 - 114154192	Apr 27, 2020 (154)
62	Qatari	NC_000023.10 - 114154192	Apr 27, 2020 (154)
63	SGDP_PRJ	NC_000023.10 - 114154192	Apr 27, 2020 (154)
64	Siberian	NC_000023.10 - 114154192	Apr 27, 2020 (154)
65	8.3KJPN	NC_000023.10 - 114154192	Apr 26, 2021 (155)
66	14KJPN	NC_000023.11 - 114919629	Oct 17, 2022 (156)
67	TopMed	NC_000023.11 - 114919629	Apr 26, 2021 (155)
68	UK 10K study - Twins	NC_000023.10 - 114154192	Oct 12, 2018 (152)
69	A Vietnamese Genetic Variation Database	NC_000023.10 - 114154192	Jul 14, 2019 (153)
70	ALFA	NC_000023.11 - 114919629	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)
rs6579555	Aug 26, 2003 (117)
rs59525646	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss78631637, ss83939138	NC_000023.8:113977171:G:A	NC_000023.11:114919628:G:A	(self)
ss113001447, ss115645293, ss204345994, ss208887150, ss256106590, ss283843924, ss287639428, ss294494350	NC_000023.9:114060447:G:A	NC_000023.11:114919628:G:A	(self)
83786162, 46162020, 9647241, 49938327, 21686882, 44112691, 11716126, 93904107, 46162020, 10150117, ss341732140, ss662977363, ss1083085027, ss1432103380, ss1555824276, ss1583482304, ss1641376073, ss1684370106, ss1939644960, ss1971421849, ss2159199772, ss2629759283, ss2710319427, ss2982533132, ss3020493219, ss3770528879, ss3836281983, ss3841745340, ss3892095711, ss3942760933, ss5235934800, ss5665751798, ss5978848461	NC_000023.10:114154191:G:A	NC_000023.11:114919628:G:A	(self)
110120763, 4023210, 132048635, 698282446, 1429116538, ss2319737580, ss3029100850, ss3651320304, ss3823309253, ss3847278504, ss5134676089, ss5313654022, ss5505098362, ss5622594828, ss5798211531, ss5819292948, ss5857172738	NC_000023.11:114919628:G:A	NC_000023.11:114919628:G:A	(self)
ss8547110, ss12051549, ss19812810, ss20388795, ss21044034	NT_028405.9:586523:G:A	NC_000023.11:114919628:G:A	(self)
ss8230461, ss80746962, ss105757647, ss133681590, ss157668105	NT_028405.12:586523:G:A	NC_000023.11:114919628:G: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 rs5946234

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

rs5946234