Name: rs200136097
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.

rs200136097

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:240462458 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000291 (77/264690, TOPMED)
T=0.000364 (51/140252, GnomAD)
T=0.000703 (75/106672, ALFA) (+ 8 more)
T=0.00041 (32/77638, ExAC)
T=0.00039 (5/12872, GO-ESP)
T=0.0002 (1/6404, 1000G_30x)
T=0.0002 (1/5008, 1000G)
T=0.0011 (5/4480, Estonian)
T=0.0005 (2/3854, ALSPAC)
T=0.0005 (2/3708, TWINSUK)
T=0.003 (3/998, GoNL)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GPC1 : 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	106794	C=0.999298	T=0.000702
European	Sub	89164	C=0.99927	T=0.00073
African	Sub	3702	C=1.0000	T=0.0000
African Others	Sub	124	C=1.000	T=0.000
African American	Sub	3578	C=1.0000	T=0.0000
Asian	Sub	194	C=1.000	T=0.000
East Asian	Sub	112	C=1.000	T=0.000
Other Asian	Sub	82	C=1.00	T=0.00
Latin American 1	Sub	500	C=1.000	T=0.000
Latin American 2	Sub	648	C=0.998	T=0.002
South Asian	Sub	98	C=1.00	T=0.00
Other	Sub	12488	C=0.99928	T=0.00072

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=0.999709	T=0.000291
gnomAD - Genomes	Global	Study-wide	140252	C=0.999636	T=0.000364
gnomAD - Genomes	European	Sub	75936	C=0.99938	T=0.00062
gnomAD - Genomes	African	Sub	42040	C=0.99993	T=0.00007
gnomAD - Genomes	American	Sub	13666	C=0.99993	T=0.00007
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=1.0000	T=0.0000
gnomAD - Genomes	East Asian	Sub	3134	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2152	C=1.0000	T=0.0000
Allele Frequency Aggregator	Total	Global	106672	C=0.999297	T=0.000703
Allele Frequency Aggregator	European	Sub	89060	C=0.99927	T=0.00073
Allele Frequency Aggregator	Other	Sub	12484	C=0.99928	T=0.00072
Allele Frequency Aggregator	African	Sub	3688	C=1.0000	T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	648	C=0.998	T=0.002
Allele Frequency Aggregator	Latin American 1	Sub	500	C=1.000	T=0.000
Allele Frequency Aggregator	Asian	Sub	194	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=1.00	T=0.00
ExAC	Global	Study-wide	77638	C=0.99959	T=0.00041
ExAC	Europe	Sub	45436	C=0.99932	T=0.00068
ExAC	Asian	Sub	18354	C=1.00000	T=0.00000
ExAC	American	Sub	7820	C=1.0000	T=0.0000
ExAC	African	Sub	5488	C=0.9998	T=0.0002
ExAC	Other	Sub	540	C=1.000	T=0.000
GO Exome Sequencing Project	Global	Study-wide	12872	C=0.99961	T=0.00039
GO Exome Sequencing Project	European American	Sub	8530	C=0.9994	T=0.0006
GO Exome Sequencing Project	African American	Sub	4342	C=1.0000	T=0.0000
1000Genomes_30x	Global	Study-wide	6404	C=0.9998	T=0.0002
1000Genomes_30x	African	Sub	1786	C=1.0000	T=0.0000
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=0.9991	T=0.0009
1000Genomes_30x	American	Sub	980	C=1.000	T=0.000
1000Genomes	Global	Study-wide	5008	C=0.9998	T=0.0002
1000Genomes	African	Sub	1322	C=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	C=0.9990	T=0.0010
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=1.000	T=0.000
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9989	T=0.0011
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9995	T=0.0005
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9995	T=0.0005
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.997	T=0.003

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 2	NC_000002.12:g.240462458C>G
GRCh38.p14 chr 2	NC_000002.12:g.240462458C>T
GRCh37.p13 chr 2	NC_000002.11:g.241401875C>G
GRCh37.p13 chr 2	NC_000002.11:g.241401875C>T

Gene: GPC1, glypican 1 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GPC1 transcript	NM_002081.3:c.593C>G	A [GCG] > G [GGG]	Coding Sequence Variant
glypican-1 precursor	NP_002072.2:p.Ala198Gly	A (Ala) > G (Gly)	Missense Variant
GPC1 transcript	NM_002081.3:c.593C>T	A [GCG] > V [GTG]	Coding Sequence Variant
glypican-1 precursor	NP_002072.2:p.Ala198Val	A (Ala) > V (Val)	Missense Variant
GPC1 transcript variant X1	XM_047443961.1:c.377C>G	A [GCG] > G [GGG]	Coding Sequence Variant
glypican-1 isoform X1	XP_047299917.1:p.Ala126Gly	A (Ala) > G (Gly)	Missense Variant
GPC1 transcript variant X1	XM_047443961.1:c.377C>T	A [GCG] > V [GTG]	Coding Sequence Variant
glypican-1 isoform X1	XP_047299917.1:p.Ala126Val	A (Ala) > V (Val)	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.

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	C=	G	T
GRCh38.p14 chr 2	NC_000002.12:g.240462458=	NC_000002.12:g.240462458C>G	NC_000002.12:g.240462458C>T
GRCh37.p13 chr 2	NC_000002.11:g.241401875=	NC_000002.11:g.241401875C>G	NC_000002.11:g.241401875C>T
GPC1 transcript	NM_002081.3:c.593=	NM_002081.3:c.593C>G	NM_002081.3:c.593C>T
GPC1 transcript	NM_002081.2:c.593=	NM_002081.2:c.593C>G	NM_002081.2:c.593C>T
GPC1 transcript variant X1	XM_047443961.1:c.377=	XM_047443961.1:c.377C>G	XM_047443961.1:c.377C>T
glypican-1 precursor	NP_002072.2:p.Ala198=	NP_002072.2:p.Ala198Gly	NP_002072.2:p.Ala198Val
glypican-1 isoform X1	XP_047299917.1:p.Ala126=	XP_047299917.1:p.Ala126Gly	XP_047299917.1:p.Ala126Val

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, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EXOME_CHIP	ss491334232	May 04, 2012 (137)
2	CLINSEQ_SNP	ss491803691	May 04, 2012 (137)
3	NHLBI-ESP	ss712486721	Apr 25, 2013 (138)
4	ILLUMINA	ss783494400	Sep 08, 2015 (146)
5	EVA-GONL	ss978149090	Aug 21, 2014 (142)
6	1000GENOMES	ss1302353564	Aug 21, 2014 (142)
7	EVA_UK10K_ALSPAC	ss1606178150	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1649172183	Apr 01, 2015 (144)
9	EVA_EXAC	ss1686821274	Apr 01, 2015 (144)
10	ILLUMINA	ss1752348178	Sep 08, 2015 (146)
11	ILLUMINA	ss1917762154	Feb 12, 2016 (147)
12	ILLUMINA	ss1946071582	Feb 12, 2016 (147)
13	ILLUMINA	ss1958524872	Feb 12, 2016 (147)
14	JJLAB	ss2021248139	Sep 14, 2016 (149)
15	HUMAN_LONGEVITY	ss2240606501	Dec 20, 2016 (150)
16	GNOMAD	ss2733466815	Nov 08, 2017 (151)
17	GNOMAD	ss2746922138	Nov 08, 2017 (151)
18	GNOMAD	ss2788302155	Nov 08, 2017 (151)
19	SWEGEN	ss2991646186	Nov 08, 2017 (151)
20	ILLUMINA	ss3022089880	Nov 08, 2017 (151)
21	ILLUMINA	ss3634820971	Oct 11, 2018 (152)
22	ILLUMINA	ss3640528269	Oct 11, 2018 (152)
23	ILLUMINA	ss3644774280	Oct 11, 2018 (152)
24	ILLUMINA	ss3652543068	Oct 11, 2018 (152)
25	EGCUT_WGS	ss3659545471	Jul 13, 2019 (153)
26	ILLUMINA	ss3744489582	Jul 13, 2019 (153)
27	ILLUMINA	ss3745120873	Jul 13, 2019 (153)
28	ILLUMINA	ss3772617207	Jul 13, 2019 (153)
29	EVA	ss3823873689	Apr 25, 2020 (154)
30	EVA	ss3986223120	Apr 27, 2021 (155)
31	TOPMED	ss4550576793	Apr 27, 2021 (155)
32	EVA	ss5337180033	Oct 17, 2022 (156)
33	HUGCELL_USP	ss5452205421	Oct 17, 2022 (156)
34	1000G_HIGH_COVERAGE	ss5530299353	Oct 17, 2022 (156)
35	EVA	ss5847910406	Oct 17, 2022 (156)
36	EVA	ss5848540223	Oct 17, 2022 (156)
37	EVA	ss5935425307	Oct 17, 2022 (156)
38	EVA	ss5957579796	Oct 17, 2022 (156)
39	1000Genomes	NC_000002.11 - 241401875	Oct 11, 2018 (152)
40	1000Genomes_30x	NC_000002.12 - 240462458	Oct 17, 2022 (156)
41	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 241401875	Oct 11, 2018 (152)
42	Genetic variation in the Estonian population	NC_000002.11 - 241401875	Oct 11, 2018 (152)
43	ExAC	NC_000002.11 - 241401875	Oct 11, 2018 (152)
44	gnomAD - Genomes	NC_000002.12 - 240462458	Apr 27, 2021 (155)
45	gnomAD - Exomes Submission ignored due to conflicting rows: Row 2536366 (NC_000002.11:241401874:C:C 228577/228578, NC_000002.11:241401874:C:G 1/228578) Row 2536367 (NC_000002.11:241401874:C:C 228511/228578, NC_000002.11:241401874:C:T 67/228578)	-	Jul 13, 2019 (153)
46	gnomAD - Exomes Submission ignored due to conflicting rows: Row 2536366 (NC_000002.11:241401874:C:C 228577/228578, NC_000002.11:241401874:C:G 1/228578) Row 2536367 (NC_000002.11:241401874:C:C 228511/228578, NC_000002.11:241401874:C:T 67/228578)	-	Jul 13, 2019 (153)
47	GO Exome Sequencing Project	NC_000002.11 - 241401875	Oct 11, 2018 (152)
48	Genome of the Netherlands Release 5	NC_000002.11 - 241401875	Apr 25, 2020 (154)
49	TopMed	NC_000002.12 - 240462458	Apr 27, 2021 (155)
50	UK 10K study - Twins	NC_000002.11 - 241401875	Oct 11, 2018 (152)
51	ALFA	NC_000002.12 - 240462458	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss2733466815	NC_000002.11:241401874:C:G	NC_000002.12:240462457:C:G	(self)
ss491803691	NC_000002.10:241050547:C:T	NC_000002.12:240462457:C:T	(self)
13484048, 7474470, 5283719, 6732234, 332084, 3275951, 7474470, ss491334232, ss712486721, ss783494400, ss978149090, ss1302353564, ss1606178150, ss1649172183, ss1686821274, ss1752348178, ss1917762154, ss1946071582, ss1958524872, ss2021248139, ss2733466815, ss2746922138, ss2788302155, ss2991646186, ss3022089880, ss3634820971, ss3640528269, ss3644774280, ss3652543068, ss3659545471, ss3744489582, ss3745120873, ss3772617207, ss3823873689, ss3986223120, ss5337180033, ss5847910406, ss5848540223, ss5957579796	NC_000002.11:241401874:C:T	NC_000002.12:240462457:C:T	(self)
17825288, 95941962, 354399672, 14777481519, ss2240606501, ss4550576793, ss5452205421, ss5530299353, ss5935425307	NC_000002.12:240462457:C:T	NC_000002.12:240462457: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 rs200136097

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

rs200136097