Name: rs5951421
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.

rs5951421

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:21352250 (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: A=0.312520 (82721/264690, TOPMED)
A=0.301574 (31085/103076, GnomAD)
A=0.16504 (3667/22219, 14KJPN) (+ 12 more)
A=0.21987 (4072/18520, ALFA)
A=0.16741 (2150/12843, 8.3KJPN)
A=0.3301 (1586/4805, 1000G_30x)
A=0.3282 (1239/3775, 1000G)
A=0.1143 (424/3708, TWINSUK)
A=0.1945 (570/2930, KOREAN)
A=0.1142 (330/2889, ALSPAC)
G=0.180 (27/150, SGDP_PRJ)
A=0.250 (27/108, Qatari)
A=0.33 (16/48, Vietnamese)
A=0.23 (9/40, GENOME_DK)
G=0.4 (3/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105373146 : 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	18520	G=0.78013	A=0.21987
European	Sub	14152	G=0.87733	A=0.12267
African	Sub	2898	G=0.2867	A=0.7133
African Others	Sub	114	G=0.237	A=0.763
African American	Sub	2784	G=0.2888	A=0.7112
Asian	Sub	112	G=0.723	A=0.277
East Asian	Sub	86	G=0.70	A=0.30
Other Asian	Sub	26	G=0.81	A=0.19
Latin American 1	Sub	146	G=0.747	A=0.253
Latin American 2	Sub	610	G=0.923	A=0.077
South Asian	Sub	98	G=0.91	A=0.09
Other	Sub	504	G=0.712	A=0.288

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=0.687480	A=0.312520
gnomAD - Genomes	Global	Study-wide	103076	G=0.698426	A=0.301574
gnomAD - Genomes	European	Sub	56788	G=0.88249	A=0.11751
gnomAD - Genomes	African	Sub	30815	G=0.29369	A=0.70631
gnomAD - Genomes	American	Sub	9243	G=0.8643	A=0.1357
gnomAD - Genomes	Ashkenazi Jewish	Sub	2511	G=0.8403	A=0.1597
gnomAD - Genomes	East Asian	Sub	2168	G=0.7385	A=0.2615
gnomAD - Genomes	Other	Sub	1551	G=0.7260	A=0.2740
14KJPN	JAPANESE	Study-wide	22219	G=0.83496	A=0.16504
Allele Frequency Aggregator	Total	Global	18520	G=0.78013	A=0.21987
Allele Frequency Aggregator	European	Sub	14152	G=0.87733	A=0.12267
Allele Frequency Aggregator	African	Sub	2898	G=0.2867	A=0.7133
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.923	A=0.077
Allele Frequency Aggregator	Other	Sub	504	G=0.712	A=0.288
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.747	A=0.253
Allele Frequency Aggregator	Asian	Sub	112	G=0.723	A=0.277
Allele Frequency Aggregator	South Asian	Sub	98	G=0.91	A=0.09
8.3KJPN	JAPANESE	Study-wide	12843	G=0.83259	A=0.16741
1000Genomes_30x	Global	Study-wide	4805	G=0.6699	A=0.3301
1000Genomes_30x	African	Sub	1328	G=0.2071	A=0.7929
1000Genomes_30x	Europe	Sub	961	G=0.866	A=0.134
1000Genomes_30x	South Asian	Sub	883	G=0.908	A=0.092
1000Genomes_30x	East Asian	Sub	878	G=0.731	A=0.269
1000Genomes_30x	American	Sub	755	G=0.885	A=0.115
1000Genomes	Global	Study-wide	3775	G=0.6718	A=0.3282
1000Genomes	African	Sub	1003	G=0.2094	A=0.7906
1000Genomes	Europe	Sub	766	G=0.863	A=0.137
1000Genomes	East Asian	Sub	764	G=0.730	A=0.270
1000Genomes	South Asian	Sub	718	G=0.907	A=0.093
1000Genomes	American	Sub	524	G=0.870	A=0.130
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.8857	A=0.1143
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.8055	A=0.1945
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	2889	G=0.8858	A=0.1142
SGDP_PRJ	Global	Study-wide	150	G=0.180	A=0.820
Qatari	Global	Study-wide	108	G=0.750	A=0.250
A Vietnamese Genetic Variation Database	Global	Study-wide	48	G=0.67	A=0.33
The Danish reference pan genome	Danish	Study-wide	40	G=0.78	A=0.23
Siberian	Global	Study-wide	8	G=0.4	A=0.6

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.21352250G>A
GRCh37.p13 chr X	NC_000023.10:g.21370368G>A

Gene: LOC105373146, uncharacterized LOC105373146 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105373146 transcript	XM_047442707.1:c.440+2173… XM_047442707.1:c.440+21733C>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	G=	A
GRCh38.p14 chr X	NC_000023.11:g.21352250=	NC_000023.11:g.21352250G>A
GRCh37.p13 chr X	NC_000023.10:g.21370368=	NC_000023.10:g.21370368G>A
LOC105373146 transcript	XM_047442707.1:c.440+21733=	XM_047442707.1:c.440+21733C>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#.

42 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8236440	Apr 21, 2003 (114)
2	BCM_SSAHASNP	ss13724819	Dec 05, 2003 (126)
3	SC_SNP	ss19083587	Feb 28, 2004 (126)
4	HGSV	ss85846319	Dec 16, 2007 (130)
5	1000GENOMES	ss112806317	Jan 25, 2009 (130)
6	1000GENOMES	ss114503571	Jan 25, 2009 (130)
7	COMPLETE_GENOMICS	ss164552916	Jul 04, 2010 (132)
8	BUSHMAN	ss204177365	Jul 04, 2010 (132)
9	GMI	ss283707275	May 04, 2012 (137)
10	PJP	ss294531800	May 09, 2011 (134)
11	1000GENOMES	ss341351668	May 09, 2011 (134)
12	TISHKOFF	ss566791253	Apr 25, 2013 (138)
13	SSMP	ss662723222	Apr 25, 2013 (138)
14	JMKIDD_LAB	ss1082822430	Aug 21, 2014 (142)
15	1000GENOMES	ss1553746941	Apr 01, 2015 (144)
16	EVA_GENOME_DK	ss1583342739	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1640444042	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1683438075	Apr 01, 2015 (144)
19	WEILL_CORNELL_DGM	ss1939194762	Feb 12, 2016 (147)
20	USC_VALOUEV	ss2158974230	Dec 20, 2016 (150)
21	HUMAN_LONGEVITY	ss2316118400	Dec 20, 2016 (150)
22	SYSTEMSBIOZJU	ss2629673675	Nov 08, 2017 (151)
23	GRF	ss2710101671	Nov 08, 2017 (151)
24	GNOMAD	ss2977088575	Nov 08, 2017 (151)
25	SWEGEN	ss3019715538	Nov 08, 2017 (151)
26	BIOINF_KMB_FNS_UNIBA	ss3646185800	Oct 12, 2018 (152)
27	EVA	ss3769979732	Jul 13, 2019 (153)
28	KHV_HUMAN_GENOMES	ss3822823624	Jul 13, 2019 (153)
29	EVA	ss3841671691	Apr 27, 2020 (154)
30	EVA	ss3847188815	Apr 27, 2020 (154)
31	SGDP_PRJ	ss3891108002	Apr 27, 2020 (154)
32	KRGDB	ss3941465244	Apr 27, 2020 (154)
33	TOPMED	ss5117364778	Apr 27, 2021 (155)
34	TOMMO_GENOMICS	ss5233775998	Apr 27, 2021 (155)
35	1000G_HIGH_COVERAGE	ss5311991130	Oct 16, 2022 (156)
36	HUGCELL_USP	ss5503717728	Oct 16, 2022 (156)
37	1000G_HIGH_COVERAGE	ss5619920436	Oct 16, 2022 (156)
38	SANFORD_IMAGENETICS	ss5664962671	Oct 16, 2022 (156)
39	TOMMO_GENOMICS	ss5795277181	Oct 16, 2022 (156)
40	YY_MCH	ss5818925526	Oct 16, 2022 (156)
41	EVA	ss5857029837	Oct 16, 2022 (156)
42	EVA	ss5977932532	Oct 16, 2022 (156)
43	1000Genomes	NC_000023.10 - 21370368	Oct 12, 2018 (152)
44	1000Genomes_30x	NC_000023.11 - 21352250	Oct 16, 2022 (156)
45	The Avon Longitudinal Study of Parents and Children	NC_000023.10 - 21370368	Oct 12, 2018 (152)
46	The Danish reference pan genome	NC_000023.10 - 21370368	Apr 27, 2020 (154)
47	gnomAD - Genomes	NC_000023.11 - 21352250	Apr 27, 2021 (155)
48	KOREAN population from KRGDB	NC_000023.10 - 21370368	Apr 27, 2020 (154)
49	Qatari	NC_000023.10 - 21370368	Apr 27, 2020 (154)
50	SGDP_PRJ	NC_000023.10 - 21370368	Apr 27, 2020 (154)
51	Siberian	NC_000023.10 - 21370368	Apr 27, 2020 (154)
52	8.3KJPN	NC_000023.10 - 21370368	Apr 27, 2021 (155)
53	14KJPN	NC_000023.11 - 21352250	Oct 16, 2022 (156)
54	TopMed	NC_000023.11 - 21352250	Apr 27, 2021 (155)
55	UK 10K study - Twins	NC_000023.10 - 21370368	Oct 12, 2018 (152)
56	A Vietnamese Genetic Variation Database	NC_000023.10 - 21370368	Jul 13, 2019 (153)
57	ALFA	NC_000023.11 - 21352250	Apr 27, 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)
rs9887600	Mar 11, 2006 (126)
rs12395353	Mar 11, 2006 (126)
rs61417688	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss85846319	NC_000023.8:21130024:G:A	NC_000023.11:21352249:G:A	(self)
ss112806317, ss114503571, ss164552916, ss204177365, ss283707275, ss294531800	NC_000023.9:21280288:G:A	NC_000023.11:21352249:G:A	(self)
81728648, 45144294, 9507676, 48642638, 21236684, 43124982, 11490584, 91745305, 45144294, 9956977, ss341351668, ss566791253, ss662723222, ss1082822430, ss1553746941, ss1583342739, ss1640444042, ss1683438075, ss1939194762, ss2158974230, ss2629673675, ss2710101671, ss2977088575, ss3019715538, ss3769979732, ss3841671691, ss3891108002, ss3941465244, ss5233775998, ss5664962671, ss5977932532	NC_000023.10:21370367:G:A	NC_000023.11:21352249:G:A	(self)
107446371, 576603912, 129114285, 680971135, 13399588128, ss2316118400, ss3646185800, ss3822823624, ss3847188815, ss5117364778, ss5311991130, ss5503717728, ss5619920436, ss5795277181, ss5818925526, ss5857029837	NC_000023.11:21352249:G:A	NC_000023.11:21352249:G:A	(self)
ss13724819, ss19083587	NT_011757.13:17336932:G:A	NC_000023.11:21352249:G:A	(self)
ss8236440	NT_167197.1:19252129:G:A	NC_000023.11:21352249: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 rs5951421

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

rs5951421