Name: rs5951431
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.

rs5951431

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrX:22334501 (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>G
Variation Type: SNV Single Nucleotide Variation
Frequency: G=0.180649 (47816/264690, TOPMED)
G=0.15774 (15110/95792, GnomAD)
G=0.44591 (9876/22148, 14KJPN) (+ 13 more)
G=0.13962 (2278/16316, ALFA)
G=0.43469 (5541/12747, 8.3KJPN)
G=0.2518 (1210/4805, 1000G_30x)
G=0.2495 (942/3775, 1000G)
G=0.0933 (346/3708, TWINSUK)
G=0.4016 (1175/2926, KOREAN)
G=0.0948 (274/2889, ALSPAC)
A=0.201 (35/174, SGDP_PRJ)
G=0.296 (32/108, Qatari)
G=0.40 (19/48, Vietnamese)
G=0.07 (3/40, GENOME_DK)
A=0.5 (3/6, Siberian)
G=0.5 (3/6, 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	16316	A=0.86038	G=0.13962
European	Sub	12064	A=0.89390	G=0.10610
African	Sub	2816	A=0.7667	G=0.2333
African Others	Sub	108	A=0.630	G=0.370
African American	Sub	2708	A=0.7722	G=0.2278
Asian	Sub	108	A=0.713	G=0.287
East Asian	Sub	84	A=0.71	G=0.29
Other Asian	Sub	24	A=0.71	G=0.29
Latin American 1	Sub	146	A=0.808	G=0.192
Latin American 2	Sub	610	A=0.731	G=0.269
South Asian	Sub	94	A=0.59	G=0.41
Other	Sub	478	A=0.835	G=0.165

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=0.819351	G=0.180649
gnomAD - Genomes	Global	Study-wide	95792	A=0.84226	G=0.15774
gnomAD - Genomes	European	Sub	53259	A=0.90612	G=0.09388
gnomAD - Genomes	African	Sub	28354	A=0.76377	G=0.23623
gnomAD - Genomes	American	Sub	8221	A=0.7235	G=0.2765
gnomAD - Genomes	Ashkenazi Jewish	Sub	2431	A=0.8885	G=0.1115
gnomAD - Genomes	East Asian	Sub	2085	A=0.7046	G=0.2954
gnomAD - Genomes	Other	Sub	1442	A=0.8252	G=0.1748
14KJPN	JAPANESE	Study-wide	22148	A=0.55409	G=0.44591
Allele Frequency Aggregator	Total	Global	16316	A=0.86038	G=0.13962
Allele Frequency Aggregator	European	Sub	12064	A=0.89390	G=0.10610
Allele Frequency Aggregator	African	Sub	2816	A=0.7667	G=0.2333
Allele Frequency Aggregator	Latin American 2	Sub	610	A=0.731	G=0.269
Allele Frequency Aggregator	Other	Sub	478	A=0.835	G=0.165
Allele Frequency Aggregator	Latin American 1	Sub	146	A=0.808	G=0.192
Allele Frequency Aggregator	Asian	Sub	108	A=0.713	G=0.287
Allele Frequency Aggregator	South Asian	Sub	94	A=0.59	G=0.41
8.3KJPN	JAPANESE	Study-wide	12747	A=0.56531	G=0.43469
1000Genomes_30x	Global	Study-wide	4805	A=0.7482	G=0.2518
1000Genomes_30x	African	Sub	1328	A=0.7026	G=0.2974
1000Genomes_30x	Europe	Sub	961	A=0.917	G=0.083
1000Genomes_30x	South Asian	Sub	883	A=0.721	G=0.279
1000Genomes_30x	East Asian	Sub	878	A=0.688	G=0.312
1000Genomes_30x	American	Sub	755	A=0.715	G=0.285
1000Genomes	Global	Study-wide	3775	A=0.7505	G=0.2495
1000Genomes	African	Sub	1003	A=0.6969	G=0.3031
1000Genomes	Europe	Sub	766	A=0.922	G=0.078
1000Genomes	East Asian	Sub	764	A=0.694	G=0.306
1000Genomes	South Asian	Sub	718	A=0.719	G=0.281
1000Genomes	American	Sub	524	A=0.729	G=0.271
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.9067	G=0.0933
KOREAN population from KRGDB	KOREAN	Study-wide	2926	A=0.5984	G=0.4016
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	2889	A=0.9052	G=0.0948
SGDP_PRJ	Global	Study-wide	174	A=0.201	G=0.799
Qatari	Global	Study-wide	108	A=0.704	G=0.296
A Vietnamese Genetic Variation Database	Global	Study-wide	48	A=0.60	G=0.40
The Danish reference pan genome	Danish	Study-wide	40	A=0.93	G=0.07
Siberian	Global	Study-wide	6	A=0.5	G=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 X	NC_000023.11:g.22334501A>G
GRCh37.p13 chr X	NC_000023.10:g.22352618A>G

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=	G
GRCh38.p14 chr X	NC_000023.11:g.22334501=	NC_000023.11:g.22334501A>G
GRCh37.p13 chr X	NC_000023.10:g.22352618=	NC_000023.10:g.22352618A>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#.

38 SubSNP, 15 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_SNP	ss8236450	Apr 21, 2003 (114)
2	CSHL-HAPMAP	ss19812117	Feb 27, 2004 (120)
3	SSAHASNP	ss21033934	Apr 05, 2004 (121)
4	ABI	ss43729394	Mar 15, 2006 (126)
5	ENSEMBL	ss144512706	Dec 01, 2009 (131)
6	GMI	ss157377146	Dec 01, 2009 (131)
7	ENSEMBL	ss161781914	Dec 01, 2009 (131)
8	GMI	ss283708612	May 04, 2012 (137)
9	PJP	ss294532344	May 09, 2011 (134)
10	1000GENOMES	ss341355902	May 09, 2011 (134)
11	TISHKOFF	ss566793590	Apr 25, 2013 (138)
12	SSMP	ss662725547	Apr 25, 2013 (138)
13	DDI	ss1432013087	Apr 01, 2015 (144)
14	1000GENOMES	ss1553767698	Apr 01, 2015 (144)
15	EVA_GENOME_DK	ss1583344180	Apr 01, 2015 (144)
16	EVA_UK10K_ALSPAC	ss1640454081	Apr 01, 2015 (144)
17	EVA_UK10K_TWINSUK	ss1683448114	Apr 01, 2015 (144)
18	WEILL_CORNELL_DGM	ss1939199040	Feb 12, 2016 (147)
19	USC_VALOUEV	ss2158976557	Dec 20, 2016 (150)
20	HUMAN_LONGEVITY	ss2316158447	Dec 20, 2016 (150)
21	GRF	ss2710103686	Nov 08, 2017 (151)
22	GNOMAD	ss2977140211	Nov 08, 2017 (151)
23	SWEGEN	ss3019722628	Nov 08, 2017 (151)
24	CSHL	ss3352915722	Nov 08, 2017 (151)
25	EVA	ss3769985329	Jul 13, 2019 (153)
26	KHV_HUMAN_GENOMES	ss3822828457	Jul 13, 2019 (153)
27	SGDP_PRJ	ss3891117409	Apr 27, 2020 (154)
28	KRGDB	ss3941476367	Apr 27, 2020 (154)
29	TOPMED	ss5117535579	Apr 26, 2021 (155)
30	TOMMO_GENOMICS	ss5233796262	Apr 26, 2021 (155)
31	1000G_HIGH_COVERAGE	ss5312007840	Oct 16, 2022 (156)
32	HUGCELL_USP	ss5503733364	Oct 16, 2022 (156)
33	1000G_HIGH_COVERAGE	ss5619946225	Oct 16, 2022 (156)
34	SANFORD_IMAGENETICS	ss5664970449	Oct 16, 2022 (156)
35	TOMMO_GENOMICS	ss5795303400	Oct 16, 2022 (156)
36	YY_MCH	ss5818929001	Oct 16, 2022 (156)
37	EVA	ss5857031338	Oct 16, 2022 (156)
38	EVA	ss5977942024	Oct 16, 2022 (156)
39	1000Genomes	NC_000023.10 - 22352618	Oct 12, 2018 (152)
40	1000Genomes_30x	NC_000023.11 - 22334501	Oct 16, 2022 (156)
41	The Avon Longitudinal Study of Parents and Children	NC_000023.10 - 22352618	Oct 12, 2018 (152)
42	The Danish reference pan genome	NC_000023.10 - 22352618	Apr 27, 2020 (154)
43	gnomAD - Genomes	NC_000023.11 - 22334501	Apr 26, 2021 (155)
44	KOREAN population from KRGDB	NC_000023.10 - 22352618	Apr 27, 2020 (154)
45	Qatari	NC_000023.10 - 22352618	Apr 27, 2020 (154)
46	SGDP_PRJ	NC_000023.10 - 22352618	Apr 27, 2020 (154)
47	Siberian	NC_000023.10 - 22352618	Apr 27, 2020 (154)
48	8.3KJPN	NC_000023.10 - 22352618	Apr 26, 2021 (155)
49	14KJPN	NC_000023.11 - 22334501	Oct 16, 2022 (156)
50	TopMed	NC_000023.11 - 22334501	Apr 26, 2021 (155)
51	UK 10K study - Twins	NC_000023.10 - 22352618	Oct 12, 2018 (152)
52	A Vietnamese Genetic Variation Database	NC_000023.10 - 22352618	Jul 13, 2019 (153)
53	ALFA	NC_000023.11 - 22334501	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
ss283708612, ss294532344	NC_000023.9:22262538:A:G	NC_000023.11:22334500:A:G	(self)
81749251, 45155287, 9509117, 48653761, 21240962, 43134389, 11492911, 91765569, 45155287, 9959091, ss341355902, ss566793590, ss662725547, ss1432013087, ss1553767698, ss1583344180, ss1640454081, ss1683448114, ss1939199040, ss2158976557, ss2710103686, ss2977140211, ss3019722628, ss3352915722, ss3769985329, ss3891117409, ss3941476367, ss5233796262, ss5664970449, ss5977942024	NC_000023.10:22352617:A:G	NC_000023.11:22334500:A:G	(self)
107472160, 576730803, 129140504, 681141936, 13586150796, ss2316158447, ss3822828457, ss5117535579, ss5312007840, ss5503733364, ss5619946225, ss5795303400, ss5818929001, ss5857031338	NC_000023.11:22334500:A:G	NC_000023.11:22334500:A:G	(self)
ss19812117, ss21033934	NT_011757.13:18319182:A:G	NC_000023.11:22334500:A:G	(self)
ss8236450, ss43729394, ss144512706, ss157377146, ss161781914	NT_167197.1:20234379:A:G	NC_000023.11:22334500:A: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 rs5951431

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

rs5951431