Name: rs5951424
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.

rs5951424

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:22283864 (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: T=0.295228 (78144/264690, TOPMED)
T=0.18854 (4190/22223, 14KJPN)
T=0.07612 (1083/14228, ALFA) (+ 12 more)
T=0.18493 (2375/12843, 8.3KJPN)
T=0.2970 (1427/4805, 1000G_30x)
T=0.2930 (1106/3775, 1000G)
T=0.1694 (628/3708, TWINSUK)
T=0.1985 (580/2922, KOREAN)
T=0.1717 (496/2889, ALSPAC)
T=0.3203 (599/1870, HapMap)
A=0.235 (38/162, SGDP_PRJ)
T=0.204 (22/108, Qatari)
T=0.08 (4/48, Vietnamese)
T=0.15 (6/40, GENOME_DK)
A=0.22 (4/18, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PTCHD1-AS : 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	14228	A=0.92388	C=0.00000, T=0.07612
European	Sub	12238	A=0.91494	C=0.00000, T=0.08506
African	Sub	992	A=0.962	C=0.000, T=0.038
African Others	Sub	30	A=0.83	C=0.00, T=0.17
African American	Sub	962	A=0.966	C=0.000, T=0.034
Asian	Sub	74	A=1.00	C=0.00, T=0.00
East Asian	Sub	60	A=1.00	C=0.00, T=0.00
Other Asian	Sub	14	A=1.00	C=0.00, T=0.00
Latin American 1	Sub	76	A=1.00	C=0.00, T=0.00
Latin American 2	Sub	454	A=1.000	C=0.000, T=0.000
South Asian	Sub	70	A=1.00	C=0.00, T=0.00
Other	Sub	324	A=0.988	C=0.000, T=0.012

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=0.704772	T=0.295228
14KJPN	JAPANESE	Study-wide	22223	A=0.81146	T=0.18854
Allele Frequency Aggregator	Total	Global	14228	A=0.92388	C=0.00000, T=0.07612
Allele Frequency Aggregator	European	Sub	12238	A=0.91494	C=0.00000, T=0.08506
Allele Frequency Aggregator	African	Sub	992	A=0.962	C=0.000, T=0.038
Allele Frequency Aggregator	Latin American 2	Sub	454	A=1.000	C=0.000, T=0.000
Allele Frequency Aggregator	Other	Sub	324	A=0.988	C=0.000, T=0.012
Allele Frequency Aggregator	Latin American 1	Sub	76	A=1.00	C=0.00, T=0.00
Allele Frequency Aggregator	Asian	Sub	74	A=1.00	C=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	70	A=1.00	C=0.00, T=0.00
8.3KJPN	JAPANESE	Study-wide	12843	A=0.81507	T=0.18493
1000Genomes_30x	Global	Study-wide	4805	A=0.7030	T=0.2970
1000Genomes_30x	African	Sub	1328	A=0.4209	T=0.5791
1000Genomes_30x	Europe	Sub	961	A=0.834	T=0.166
1000Genomes_30x	South Asian	Sub	883	A=0.814	T=0.186
1000Genomes_30x	East Asian	Sub	878	A=0.798	T=0.202
1000Genomes_30x	American	Sub	755	A=0.792	T=0.208
1000Genomes	Global	Study-wide	3775	A=0.7070	T=0.2930
1000Genomes	African	Sub	1003	A=0.4148	T=0.5852
1000Genomes	Europe	Sub	766	A=0.833	T=0.167
1000Genomes	East Asian	Sub	764	A=0.805	T=0.195
1000Genomes	South Asian	Sub	718	A=0.819	T=0.181
1000Genomes	American	Sub	524	A=0.786	T=0.214
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.8306	T=0.1694
KOREAN population from KRGDB	KOREAN	Study-wide	2922	A=0.8015	G=0.0000, T=0.1985
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	2889	A=0.8283	T=0.1717
HapMap	Global	Study-wide	1870	A=0.6797	T=0.3203
HapMap	American	Sub	764	A=0.776	T=0.224
HapMap	African	Sub	680	A=0.481	T=0.519
HapMap	Asian	Sub	254	A=0.843	T=0.157
HapMap	Europe	Sub	172	A=0.797	T=0.203
SGDP_PRJ	Global	Study-wide	162	A=0.235	T=0.765
Qatari	Global	Study-wide	108	A=0.796	T=0.204
A Vietnamese Genetic Variation Database	Global	Study-wide	48	A=0.92	T=0.08
The Danish reference pan genome	Danish	Study-wide	40	A=0.85	T=0.15
Siberian	Global	Study-wide	18	A=0.22	T=0.78

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.22283864A>C
GRCh38.p14 chr X	NC_000023.11:g.22283864A>G
GRCh38.p14 chr X	NC_000023.11:g.22283864A>T
GRCh37.p13 chr X	NC_000023.10:g.22301981A>C
GRCh37.p13 chr X	NC_000023.10:g.22301981A>G
GRCh37.p13 chr X	NC_000023.10:g.22301981A>T

Gene: PTCHD1-AS, PTCHD1 antisense RNA (head to head) (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PTCHD1-AS transcript	NR_073010.2:n.	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 X	NC_000023.11:g.22283864=	NC_000023.11:g.22283864A>C	NC_000023.11:g.22283864A>G	NC_000023.11:g.22283864A>T
GRCh37.p13 chr X	NC_000023.10:g.22301981=	NC_000023.10:g.22301981A>C	NC_000023.10:g.22301981A>G	NC_000023.10:g.22301981A>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#.

52 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8236443	Apr 21, 2003 (114)
2	BCM_SSAHASNP	ss10571965	Jul 11, 2003 (117)
3	SSAHASNP	ss20995748	Apr 05, 2004 (121)
4	PERLEGEN	ss23824806	Sep 20, 2004 (123)
5	ABI	ss43865748	Mar 13, 2006 (126)
6	AFFY	ss74851035	Aug 16, 2007 (128)
7	AFFY	ss76512046	Dec 06, 2007 (129)
8	HGSV	ss80901817	Dec 15, 2007 (130)
9	HGSV	ss85797646	Dec 15, 2007 (130)
10	KRIBB_YJKIM	ss104914949	Feb 05, 2009 (130)
11	1000GENOMES	ss114508113	Jan 25, 2009 (130)
12	ILLUMINA-UK	ss115597688	Feb 05, 2009 (130)
13	ENSEMBL	ss143583998	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss164560719	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss166124955	Jul 04, 2010 (132)
16	BUSHMAN	ss204179187	Jul 04, 2010 (132)
17	BL	ss255936874	May 09, 2011 (134)
18	GMI	ss283708451	May 04, 2012 (137)
19	PJP	ss294532279	May 09, 2011 (134)
20	1000GENOMES	ss341355512	May 09, 2011 (134)
21	TISHKOFF	ss566793359	Apr 25, 2013 (138)
22	SSMP	ss662725318	Apr 25, 2013 (138)
23	JMKIDD_LAB	ss1082825271	Aug 21, 2014 (142)
24	1000GENOMES	ss1553766312	Apr 01, 2015 (144)
25	EVA_GENOME_DK	ss1583343972	Apr 01, 2015 (144)
26	EVA_UK10K_ALSPAC	ss1640453400	Apr 01, 2015 (144)
27	EVA_UK10K_TWINSUK	ss1683447433	Apr 01, 2015 (144)
28	WEILL_CORNELL_DGM	ss1939198684	Feb 12, 2016 (147)
29	GENOMED	ss1971351493	Jul 19, 2016 (147)
30	USC_VALOUEV	ss2158976335	Dec 20, 2016 (150)
31	HUMAN_LONGEVITY	ss2316155986	Dec 20, 2016 (150)
32	SYSTEMSBIOZJU	ss2629674424	Nov 08, 2017 (151)
33	GRF	ss2710103483	Nov 08, 2017 (151)
34	GNOMAD	ss2977137159	Nov 08, 2017 (151)
35	SWEGEN	ss3019722081	Nov 08, 2017 (151)
36	BIOINF_KMB_FNS_UNIBA	ss3029016701	Nov 08, 2017 (151)
37	URBANLAB	ss3651254843	Oct 12, 2018 (152)
38	EVA	ss3769984875	Jul 13, 2019 (153)
39	KHV_HUMAN_GENOMES	ss3822828031	Jul 13, 2019 (153)
40	EVA	ss3836112357	Apr 27, 2020 (154)
41	SGDP_PRJ	ss3891116690	Apr 27, 2020 (154)
42	KRGDB	ss3941475703	Apr 27, 2020 (154)
43	TOPMED	ss5117525937	Apr 26, 2021 (155)
44	TOMMO_GENOMICS	ss5233795031	Apr 26, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5312006709	Oct 16, 2022 (156)
46	HUGCELL_USP	ss5503732325	Oct 16, 2022 (156)
47	1000G_HIGH_COVERAGE	ss5619944613	Oct 16, 2022 (156)
48	SANFORD_IMAGENETICS	ss5664969851	Oct 16, 2022 (156)
49	TOMMO_GENOMICS	ss5795301849	Oct 16, 2022 (156)
50	YY_MCH	ss5818928661	Oct 16, 2022 (156)
51	EVA	ss5857031175	Oct 16, 2022 (156)
52	EVA	ss5977941336	Oct 16, 2022 (156)
53	1000Genomes	NC_000023.10 - 22301981	Oct 12, 2018 (152)
54	1000Genomes_30x	NC_000023.11 - 22283864	Oct 16, 2022 (156)
55	The Avon Longitudinal Study of Parents and Children	NC_000023.10 - 22301981	Oct 12, 2018 (152)
56	The Danish reference pan genome	NC_000023.10 - 22301981	Apr 27, 2020 (154)
57	gnomAD - Genomes Submission ignored due to conflicting rows: Row 576723712 (NC_000023.11:22283863:A:C 1/103009) Row 576723713 (NC_000023.11:22283863:A:T 29062/102953)	-	Apr 26, 2021 (155)
58	gnomAD - Genomes Submission ignored due to conflicting rows: Row 576723712 (NC_000023.11:22283863:A:C 1/103009) Row 576723713 (NC_000023.11:22283863:A:T 29062/102953)	-	Apr 26, 2021 (155)
59	HapMap	NC_000023.11 - 22283864	Apr 27, 2020 (154)
60	KOREAN population from KRGDB	NC_000023.10 - 22301981	Apr 27, 2020 (154)
61	Qatari	NC_000023.10 - 22301981	Apr 27, 2020 (154)
62	SGDP_PRJ	NC_000023.10 - 22301981	Apr 27, 2020 (154)
63	Siberian	NC_000023.10 - 22301981	Apr 27, 2020 (154)
64	8.3KJPN	NC_000023.10 - 22301981	Apr 26, 2021 (155)
65	14KJPN	NC_000023.11 - 22283864	Oct 16, 2022 (156)
66	TopMed	NC_000023.11 - 22283864	Apr 26, 2021 (155)
67	UK 10K study - Twins	NC_000023.10 - 22301981	Oct 12, 2018 (152)
68	A Vietnamese Genetic Variation Database	NC_000023.10 - 22301981	Jul 13, 2019 (153)
69	ALFA	NC_000023.11 - 22283864	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)
rs7062784	Aug 26, 2003 (117)
rs52793244	Sep 21, 2007 (128)
rs58542865	May 24, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
2855351095	NC_000023.11:22283863:A:C	NC_000023.11:22283863:A:C	(self)
48653097, ss3941475703	NC_000023.10:22301980:A:G	NC_000023.11:22283863:A:G	(self)
ss80901817, ss85797646	NC_000023.8:22061637:A:T	NC_000023.11:22283863:A:T	(self)
ss76512046, ss114508113, ss115597688, ss164560719, ss166124955, ss204179187, ss255936874, ss283708451, ss294532279	NC_000023.9:22211901:A:T	NC_000023.11:22283863:A:T	(self)
81747878, 45154529, 9508909, 48653097, 21240606, 43133670, 11492689, 91764338, 45154529, 9958889, ss341355512, ss566793359, ss662725318, ss1082825271, ss1553766312, ss1583343972, ss1640453400, ss1683447433, ss1939198684, ss1971351493, ss2158976335, ss2629674424, ss2710103483, ss2977137159, ss3019722081, ss3769984875, ss3836112357, ss3891116690, ss3941475703, ss5233795031, ss5664969851, ss5977941336	NC_000023.10:22301980:A:T	NC_000023.11:22283863:A:T	(self)
107470548, 3957185, 129138953, 681132294, 2855351095, ss2316155986, ss3029016701, ss3651254843, ss3822828031, ss5117525937, ss5312006709, ss5503732325, ss5619944613, ss5795301849, ss5818928661, ss5857031175	NC_000023.11:22283863:A:T	NC_000023.11:22283863:A:T	(self)
ss10571965	NT_011757.12:9216447:A:T	NC_000023.11:22283863:A:T	(self)
ss20995748	NT_011757.13:18268545:A:T	NC_000023.11:22283863:A:T	(self)
ss8236443, ss23824806, ss43865748, ss74851035, ss104914949, ss143583998	NT_167197.1:20183742:A:T	NC_000023.11:22283863: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 rs5951424

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

rs5951424