Name: rs142594314
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.

rs142594314

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:115663979 (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: C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.001269 (336/264690, TOPMED)
T=0.000585 (147/251494, GnomAD_exome)
T=0.000472 (94/199278, ALFA) (+ 12 more)
T=0.001284 (180/140232, GnomAD)
T=0.000577 (70/121412, ExAC)
T=0.00161 (127/78702, PAGE_STUDY)
T=0.00177 (23/13006, GO-ESP)
T=0.0016 (10/6404, 1000G_30x)
T=0.0016 (8/5008, 1000G)
T=0.0008 (3/3854, ALSPAC)
T=0.0003 (1/3708, TWINSUK)
T=0.001 (1/998, GoNL)
T=0.005 (1/216, Qatari)
C=0.5 (1/2, SGDP_PRJ)
T=0.5 (1/2, SGDP_PRJ)

Clinical Significance: Reported in ClinVar
Gene : Consequence: VANGL1 : Missense 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	215690	C=0.999467	T=0.000533
European	Sub	180078	C=0.999595	T=0.000405
African	Sub	9792	C=0.9967	T=0.0033
African Others	Sub	360	C=0.992	T=0.008
African American	Sub	9432	C=0.9969	T=0.0031
Asian	Sub	6350	C=1.0000	T=0.0000
East Asian	Sub	4502	C=1.0000	T=0.0000
Other Asian	Sub	1848	C=1.0000	T=0.0000
Latin American 1	Sub	796	C=0.997	T=0.003
Latin American 2	Sub	968	C=0.998	T=0.002
South Asian	Sub	280	C=1.000	T=0.000
Other	Sub	17426	C=0.99966	T=0.00034

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	C=0.998731	T=0.001269
gnomAD - Exomes	Global	Study-wide	251494	C=0.999415	T=0.000585
gnomAD - Exomes	European	Sub	135416	C=0.999638	T=0.000362
gnomAD - Exomes	Asian	Sub	49010	C=0.99998	T=0.00002
gnomAD - Exomes	American	Sub	34592	C=0.99867	T=0.00133
gnomAD - Exomes	African	Sub	16256	C=0.99742	T=0.00258
gnomAD - Exomes	Ashkenazi Jewish	Sub	10080	C=1.00000	T=0.00000
gnomAD - Exomes	Other	Sub	6140	C=0.9985	T=0.0015
Allele Frequency Aggregator	Total	Global	199278	C=0.999528	T=0.000472
Allele Frequency Aggregator	European	Sub	169938	C=0.999594	T=0.000406
Allele Frequency Aggregator	Other	Sub	15992	C=0.99975	T=0.00025
Allele Frequency Aggregator	Asian	Sub	6350	C=1.0000	T=0.0000
Allele Frequency Aggregator	African	Sub	4954	C=0.9966	T=0.0034
Allele Frequency Aggregator	Latin American 2	Sub	968	C=0.998	T=0.002
Allele Frequency Aggregator	Latin American 1	Sub	796	C=0.997	T=0.003
Allele Frequency Aggregator	South Asian	Sub	280	C=1.000	T=0.000
gnomAD - Genomes	Global	Study-wide	140232	C=0.998716	T=0.001284
gnomAD - Genomes	European	Sub	75932	C=0.99958	T=0.00042
gnomAD - Genomes	African	Sub	42038	C=0.99688	T=0.00312
gnomAD - Genomes	American	Sub	13652	C=0.99912	T=0.00088
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3134	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2154	C=0.9977	T=0.0023
ExAC	Global	Study-wide	121412	C=0.999423	T=0.000577
ExAC	Europe	Sub	73354	C=0.99958	T=0.00042
ExAC	Asian	Sub	25166	C=1.00000	T=0.00000
ExAC	American	Sub	11578	C=0.99905	T=0.00095
ExAC	African	Sub	10406	C=0.99731	T=0.00269
ExAC	Other	Sub	908	C=1.000	T=0.000
The PAGE Study	Global	Study-wide	78702	C=0.99839	T=0.00161
The PAGE Study	AfricanAmerican	Sub	32516	C=0.99729	T=0.00271
The PAGE Study	Mexican	Sub	10810	C=0.99852	T=0.00148
The PAGE Study	Asian	Sub	8318	C=1.0000	T=0.0000
The PAGE Study	PuertoRican	Sub	7918	C=0.9996	T=0.0004
The PAGE Study	NativeHawaiian	Sub	4534	C=0.9996	T=0.0004
The PAGE Study	Cuban	Sub	4230	C=0.9979	T=0.0021
The PAGE Study	Dominican	Sub	3828	C=0.9995	T=0.0005
The PAGE Study	CentralAmerican	Sub	2450	C=0.9980	T=0.0020
The PAGE Study	SouthAmerican	Sub	1982	C=0.9990	T=0.0010
The PAGE Study	NativeAmerican	Sub	1260	C=1.0000	T=0.0000
The PAGE Study	SouthAsian	Sub	856	C=1.000	T=0.000
GO Exome Sequencing Project	Global	Study-wide	13006	C=0.99823	T=0.00177
GO Exome Sequencing Project	European American	Sub	8600	C=0.9992	T=0.0008
GO Exome Sequencing Project	African American	Sub	4406	C=0.9964	T=0.0036
1000Genomes_30x	Global	Study-wide	6404	C=0.9984	T=0.0016
1000Genomes_30x	African	Sub	1786	C=0.9950	T=0.0050
1000Genomes_30x	Europe	Sub	1266	C=1.0000	T=0.0000
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	T=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.999	T=0.001
1000Genomes	Global	Study-wide	5008	C=0.9984	T=0.0016
1000Genomes	African	Sub	1322	C=0.9947	T=0.0053
1000Genomes	East Asian	Sub	1008	C=1.0000	T=0.0000
1000Genomes	Europe	Sub	1006	C=1.0000	T=0.0000
1000Genomes	South Asian	Sub	978	C=1.000	T=0.000
1000Genomes	American	Sub	694	C=0.999	T=0.001
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9992	T=0.0008
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9997	T=0.0003
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.999	T=0.001
Qatari	Global	Study-wide	216	C=0.995	T=0.005
SGDP_PRJ	Global	Study-wide	2	C=0.5	T=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 1	NC_000001.11:g.115663979C>T
GRCh37.p13 chr 1	NC_000001.10:g.116206600C>T
VANGL1 RefSeqGene	NG_016548.1:g.27027C>T

Gene: VANGL1, VANGL planar cell polarity protein 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
VANGL1 transcript variant 1	NM_138959.3:c.523C>T	R [CGG] > W [TGG]	Coding Sequence Variant
vang-like protein 1 isoform 1	NP_620409.1:p.Arg175Trp	R (Arg) > W (Trp)	Missense Variant
VANGL1 transcript variant 3	NM_001172411.2:c.517C>T	R [CGG] > W [TGG]	Coding Sequence Variant
vang-like protein 1 isoform 2	NP_001165882.1:p.Arg173Trp	R (Arg) > W (Trp)	Missense Variant
VANGL1 transcript variant 2	NM_001172412.2:c.523C>T	R [CGG] > W [TGG]	Coding Sequence Variant
vang-like protein 1 isoform 1	NP_001165883.1:p.Arg175Trp	R (Arg) > W (Trp)	Missense 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.

Allele: T (allele ID: 176924 )

ClinVar Accession	Disease Names	Clinical Significance
RCV000154114.6	not provided	Uncertain-Significance
RCV000735371.2	Abnormal pulmonary interstitial morphology,Absent epiphyses,Chronic lung disease,Cleft palate,Clubfoot,Coat hanger sign of ribs,Hemivertebrae,Micrognathia,Patent ductus arteriosus,Preaxial foot polydactyly,Pseudoarthrosis,Respiratory failure,Short femur,Skeletal dysplasia,Vertebral hypoplasia,Vertebral segmentation defect	Uncertain-Significance
RCV001097604.3	Sacral defect with anterior meningocele	Benign
RCV001097605.3	Neural tube defect	Uncertain-Significance

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	C=	T
GRCh38.p14 chr 1	NC_000001.11:g.115663979=	NC_000001.11:g.115663979C>T
GRCh37.p13 chr 1	NC_000001.10:g.116206600=	NC_000001.10:g.116206600C>T
VANGL1 RefSeqGene	NG_016548.1:g.27027=	NG_016548.1:g.27027C>T
VANGL1 transcript variant 1	NM_138959.3:c.523=	NM_138959.3:c.523C>T
VANGL1 transcript variant 1	NM_138959.2:c.523=	NM_138959.2:c.523C>T
VANGL1 transcript variant 3	NM_001172411.2:c.517=	NM_001172411.2:c.517C>T
VANGL1 transcript variant 3	NM_001172411.1:c.517=	NM_001172411.1:c.517C>T
VANGL1 transcript variant 2	NM_001172412.2:c.523=	NM_001172412.2:c.523C>T
VANGL1 transcript variant 2	NM_001172412.1:c.523=	NM_001172412.1:c.523C>T
vang-like protein 1 isoform 1	NP_620409.1:p.Arg175=	NP_620409.1:p.Arg175Trp
vang-like protein 1 isoform 2	NP_001165882.1:p.Arg173=	NP_001165882.1:p.Arg173Trp
vang-like protein 1 isoform 1	NP_001165883.1:p.Arg175=	NP_001165883.1:p.Arg175Trp

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#.

50 SubSNP, 14 Frequency, 4 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss328876346	May 09, 2011 (134)
2	NHLBI-ESP	ss341983953	May 09, 2011 (134)
3	1000GENOMES	ss489759141	May 04, 2012 (137)
4	EXOME_CHIP	ss491298805	May 04, 2012 (137)
5	ILLUMINA	ss780892217	Sep 08, 2015 (146)
6	ILLUMINA	ss783578631	Sep 08, 2015 (146)
7	EVA-GONL	ss975602003	Aug 21, 2014 (142)
8	1000GENOMES	ss1292552334	Aug 21, 2014 (142)
9	EVA_DECODE	ss1584983572	Apr 01, 2015 (144)
10	EVA_UK10K_ALSPAC	ss1601055239	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1644049272	Apr 01, 2015 (144)
12	EVA_EXAC	ss1685705472	Apr 01, 2015 (144)
13	ILLUMINA	ss1751865410	Sep 08, 2015 (146)
14	ILLUMINA	ss1917733065	Feb 12, 2016 (147)
15	WEILL_CORNELL_DGM	ss1918800936	Feb 12, 2016 (147)
16	ILLUMINA	ss1946005978	Feb 12, 2016 (147)
17	ILLUMINA	ss1958305812	Feb 12, 2016 (147)
18	HUMAN_LONGEVITY	ss2165964315	Dec 20, 2016 (150)
19	GNOMAD	ss2731741425	Nov 08, 2017 (151)
20	GNOMAD	ss2746402721	Nov 08, 2017 (151)
21	GNOMAD	ss2759904346	Nov 08, 2017 (151)
22	AFFY	ss2984872019	Nov 08, 2017 (151)
23	ILLUMINA	ss3021124027	Nov 08, 2017 (151)
24	ILLUMINA	ss3626189947	Oct 11, 2018 (152)
25	ILLUMINA	ss3634344837	Oct 11, 2018 (152)
26	ILLUMINA	ss3640052196	Oct 11, 2018 (152)
27	ILLUMINA	ss3644501951	Oct 11, 2018 (152)
28	ILLUMINA	ss3651457006	Oct 11, 2018 (152)
29	ILLUMINA	ss3653644087	Oct 11, 2018 (152)
30	EVA_DECODE	ss3687589938	Jul 12, 2019 (153)
31	ILLUMINA	ss3725057417	Jul 12, 2019 (153)
32	ILLUMINA	ss3744350186	Jul 12, 2019 (153)
33	ILLUMINA	ss3744645782	Jul 12, 2019 (153)
34	PAGE_CC	ss3770835186	Jul 12, 2019 (153)
35	ILLUMINA	ss3772146969	Jul 12, 2019 (153)
36	EVA	ss3823645155	Apr 25, 2020 (154)
37	EVA	ss3825572623	Apr 25, 2020 (154)
38	SGDP_PRJ	ss3849710811	Apr 25, 2020 (154)
39	TOPMED	ss4464680648	Apr 25, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5243712688	Oct 12, 2022 (156)
41	EVA	ss5321374949	Oct 12, 2022 (156)
42	HUGCELL_USP	ss5444626423	Oct 12, 2022 (156)
43	1000G_HIGH_COVERAGE	ss5516760027	Oct 12, 2022 (156)
44	SANFORD_IMAGENETICS	ss5624216157	Oct 12, 2022 (156)
45	SANFORD_IMAGENETICS	ss5626357126	Oct 12, 2022 (156)
46	EVA	ss5832524383	Oct 12, 2022 (156)
47	EVA	ss5847552401	Oct 12, 2022 (156)
48	EVA	ss5909921006	Oct 12, 2022 (156)
49	EVA	ss5938226539	Oct 12, 2022 (156)
50	EVA	ss5979287087	Oct 12, 2022 (156)
51	1000Genomes	NC_000001.10 - 116206600	Oct 11, 2018 (152)
52	1000Genomes_30x	NC_000001.11 - 115663979	Oct 12, 2022 (156)
53	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 116206600	Oct 11, 2018 (152)
54	ExAC	NC_000001.10 - 116206600	Oct 11, 2018 (152)
55	gnomAD - Genomes	NC_000001.11 - 115663979	Apr 25, 2021 (155)
56	gnomAD - Exomes	NC_000001.10 - 116206600	Jul 12, 2019 (153)
57	GO Exome Sequencing Project	NC_000001.10 - 116206600	Oct 11, 2018 (152)
58	Genome of the Netherlands Release 5	NC_000001.10 - 116206600	Apr 25, 2020 (154)
59	The PAGE Study	NC_000001.11 - 115663979	Jul 12, 2019 (153)
60	Qatari	NC_000001.10 - 116206600	Apr 25, 2020 (154)
61	SGDP_PRJ	NC_000001.10 - 116206600	Apr 25, 2020 (154)
62	TopMed	NC_000001.11 - 115663979	Apr 25, 2021 (155)
63	UK 10K study - Twins	NC_000001.10 - 116206600	Oct 11, 2018 (152)
64	ALFA	NC_000001.11 - 115663979	Apr 25, 2021 (155)
65	ClinVar	RCV000154114.6	Oct 12, 2022 (156)
66	ClinVar	RCV000735371.2	Oct 12, 2022 (156)
67	ClinVar	RCV001097604.3	Oct 12, 2022 (156)
68	ClinVar	RCV001097605.3	Oct 12, 2022 (156)

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
ss1584983572	NC_000001.9:116008122:C:T	NC_000001.11:115663978:C:T	(self)
3332491, 1845359, 4916066, 765803, 103779, 802485, 842866, 1727791, 1845359, ss328876346, ss341983953, ss489759141, ss491298805, ss780892217, ss783578631, ss975602003, ss1292552334, ss1601055239, ss1644049272, ss1685705472, ss1751865410, ss1917733065, ss1918800936, ss1946005978, ss1958305812, ss2731741425, ss2746402721, ss2759904346, ss2984872019, ss3021124027, ss3626189947, ss3634344837, ss3640052196, ss3644501951, ss3651457006, ss3653644087, ss3744350186, ss3744645782, ss3772146969, ss3823645155, ss3825572623, ss3849710811, ss5321374949, ss5624216157, ss5626357126, ss5832524383, ss5847552401, ss5938226539, ss5979287087	NC_000001.10:116206599:C:T	NC_000001.11:115663978:C:T	(self)
RCV000154114.6, RCV000735371.2, RCV001097604.3, RCV001097605.3, 4285962, 23573277, 56655, 28286983, 11239855620, ss2165964315, ss3687589938, ss3725057417, ss3770835186, ss4464680648, ss5243712688, ss5444626423, ss5516760027, ss5909921006	NC_000001.11:115663978:C:T	NC_000001.11:115663978:C: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 rs142594314

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
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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

rs142594314