Name: rs34778053
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.

rs34778053

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:240630325 (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>A / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.01332 (445/33420, ALFA)
A=0.01960 (254/12962, GO-ESP)
A=0.0120 (77/6404, 1000G_30x) (+ 11 more)
A=0.0128 (64/5008, 1000G)
A=0.0223 (100/4480, Estonian)
A=0.0280 (108/3854, ALSPAC)
A=0.0307 (114/3708, TWINSUK)
A=0.0007 (2/2922, KOREAN)
A=0.030 (18/600, NorthernSweden)
A=0.009 (2/216, Qatari)
C=0.5 (5/10, SGDP_PRJ)
A=0.5 (5/10, SGDP_PRJ)
C=0.5 (2/4, Siberian)
A=0.5 (2/4, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: GPR35 : 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	33420	C=0.98662	A=0.01332, T=0.00006
European	Sub	25788	C=0.98503	A=0.01493, T=0.00004
African	Sub	3438	C=0.9977	A=0.0020, T=0.0003
African Others	Sub	118	C=1.000	A=0.000, T=0.000
African American	Sub	3320	C=0.9976	A=0.0021, T=0.0003
Asian	Sub	166	C=0.994	A=0.006, T=0.000
East Asian	Sub	110	C=1.000	A=0.000, T=0.000
Other Asian	Sub	56	C=0.98	A=0.02, T=0.00
Latin American 1	Sub	146	C=1.000	A=0.000, T=0.000
Latin American 2	Sub	596	C=1.000	A=0.000, T=0.000
South Asian	Sub	94	C=1.00	A=0.00, T=0.00
Other	Sub	3192	C=0.9837	A=0.0163, T=0.0000

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
Allele Frequency Aggregator	Total	Global	33420	C=0.98662	A=0.01332, T=0.00006
Allele Frequency Aggregator	European	Sub	25788	C=0.98503	A=0.01493, T=0.00004
Allele Frequency Aggregator	African	Sub	3438	C=0.9977	A=0.0020, T=0.0003
Allele Frequency Aggregator	Other	Sub	3192	C=0.9837	A=0.0163, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	596	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	166	C=0.994	A=0.006, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	South Asian	Sub	94	C=1.00	A=0.00, T=0.00
GO Exome Sequencing Project	Global	Study-wide	12962	C=0.98040	A=0.01960
GO Exome Sequencing Project	European American	Sub	8582	C=0.9768	A=0.0232
GO Exome Sequencing Project	African American	Sub	4380	C=0.9874	A=0.0126
1000Genomes_30x	Global	Study-wide	6404	C=0.9877	A=0.0120, T=0.0003
1000Genomes_30x	African	Sub	1786	C=0.9882	A=0.0112, T=0.0006
1000Genomes_30x	Europe	Sub	1266	C=0.9755	A=0.0245, T=0.0000
1000Genomes_30x	South Asian	Sub	1202	C=0.9884	A=0.0116, T=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=0.9991	A=0.0000, T=0.0009
1000Genomes_30x	American	Sub	980	C=0.988	A=0.012, T=0.000
1000Genomes	Global	Study-wide	5008	C=0.9868	A=0.0128, T=0.0004
1000Genomes	African	Sub	1322	C=0.9879	A=0.0113, T=0.0008
1000Genomes	East Asian	Sub	1008	C=0.9990	A=0.0000, T=0.0010
1000Genomes	Europe	Sub	1006	C=0.9732	A=0.0268, T=0.0000
1000Genomes	South Asian	Sub	978	C=0.986	A=0.014, T=0.000
1000Genomes	American	Sub	694	C=0.988	A=0.012, T=0.000
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9777	A=0.0223
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9720	A=0.0280
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9693	A=0.0307
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9993	A=0.0007
Northern Sweden	ACPOP	Study-wide	600	C=0.970	A=0.030
Qatari	Global	Study-wide	216	C=0.991	A=0.009
SGDP_PRJ	Global	Study-wide	10	C=0.5	A=0.5
Siberian	Global	Study-wide	4	C=0.5	A=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 2	NC_000002.12:g.240630325C>A
GRCh38.p14 chr 2	NC_000002.12:g.240630325C>T
GRCh37.p13 chr 2	NC_000002.11:g.241569742C>A
GRCh37.p13 chr 2	NC_000002.11:g.241569742C>T
LOC122889014 genomic region	NG_077146.1:g.314C>A
LOC122889014 genomic region	NG_077146.1:g.314C>T

Gene: GPR35, G protein-coupled receptor 35 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
GPR35 transcript variant 2	NM_001195381.3:c.466C>A	R [CGC] > S [AGC]	Coding Sequence Variant
G-protein coupled receptor 35 isoform b	NP_001182310.1:p.Arg156Ser	R (Arg) > S (Ser)	Missense Variant
GPR35 transcript variant 2	NM_001195381.3:c.466C>T	R [CGC] > C [TGC]	Coding Sequence Variant
G-protein coupled receptor 35 isoform b	NP_001182310.1:p.Arg156Cys	R (Arg) > C (Cys)	Missense Variant
GPR35 transcript variant 1	NM_005301.5:c.373C>A	R [CGC] > S [AGC]	Coding Sequence Variant
G-protein coupled receptor 35 isoform a	NP_005292.2:p.Arg125Ser	R (Arg) > S (Ser)	Missense Variant
GPR35 transcript variant 1	NM_005301.5:c.373C>T	R [CGC] > C [TGC]	Coding Sequence Variant
G-protein coupled receptor 35 isoform a	NP_005292.2:p.Arg125Cys	R (Arg) > C (Cys)	Missense Variant
GPR35 transcript variant 3	NM_001195382.3:c.466C>A	R [CGC] > S [AGC]	Coding Sequence Variant
G-protein coupled receptor 35 isoform b	NP_001182311.1:p.Arg156Ser	R (Arg) > S (Ser)	Missense Variant
GPR35 transcript variant 3	NM_001195382.3:c.466C>T	R [CGC] > C [TGC]	Coding Sequence Variant
G-protein coupled receptor 35 isoform b	NP_001182311.1:p.Arg156Cys	R (Arg) > C (Cys)	Missense Variant
GPR35 transcript variant 4	NM_001394730.1:c.466C>A	R [CGC] > S [AGC]	Coding Sequence Variant
G-protein coupled receptor 35 isoform b	NP_001381659.1:p.Arg156Ser	R (Arg) > S (Ser)	Missense Variant
GPR35 transcript variant 4	NM_001394730.1:c.466C>T	R [CGC] > C [TGC]	Coding Sequence Variant
G-protein coupled receptor 35 isoform b	NP_001381659.1:p.Arg156Cys	R (Arg) > C (Cys)	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=	A	T
GRCh38.p14 chr 2	NC_000002.12:g.240630325=	NC_000002.12:g.240630325C>A	NC_000002.12:g.240630325C>T
GRCh37.p13 chr 2	NC_000002.11:g.241569742=	NC_000002.11:g.241569742C>A	NC_000002.11:g.241569742C>T
LOC122889014 genomic region	NG_077146.1:g.314=	NG_077146.1:g.314C>A	NG_077146.1:g.314C>T
GPR35 transcript variant 1	NM_005301.5:c.373=	NM_005301.5:c.373C>A	NM_005301.5:c.373C>T
GPR35 transcript variant 1	NM_005301.4:c.373=	NM_005301.4:c.373C>A	NM_005301.4:c.373C>T
GPR35 transcript variant 1	NM_005301.3:c.373=	NM_005301.3:c.373C>A	NM_005301.3:c.373C>T
GPR35 transcript variant 2	NM_001195381.3:c.466=	NM_001195381.3:c.466C>A	NM_001195381.3:c.466C>T
GPR35 transcript variant 2	NM_001195381.2:c.466=	NM_001195381.2:c.466C>A	NM_001195381.2:c.466C>T
GPR35 transcript variant 2	NM_001195381.1:c.466=	NM_001195381.1:c.466C>A	NM_001195381.1:c.466C>T
GPR35 transcript variant 3	NM_001195382.3:c.466=	NM_001195382.3:c.466C>A	NM_001195382.3:c.466C>T
GPR35 transcript variant 3	NM_001195382.2:c.466=	NM_001195382.2:c.466C>A	NM_001195382.2:c.466C>T
GPR35 transcript variant 3	NM_001195382.1:c.466=	NM_001195382.1:c.466C>A	NM_001195382.1:c.466C>T
GPR35 transcript variant 4	NM_001394730.1:c.466=	NM_001394730.1:c.466C>A	NM_001394730.1:c.466C>T
G-protein coupled receptor 35 isoform a	NP_005292.2:p.Arg125=	NP_005292.2:p.Arg125Ser	NP_005292.2:p.Arg125Cys
G-protein coupled receptor 35 isoform b	NP_001182310.1:p.Arg156=	NP_001182310.1:p.Arg156Ser	NP_001182310.1:p.Arg156Cys
G-protein coupled receptor 35 isoform b	NP_001182311.1:p.Arg156=	NP_001182311.1:p.Arg156Ser	NP_001182311.1:p.Arg156Cys
G-protein coupled receptor 35 isoform b	NP_001381659.1:p.Arg156=	NP_001381659.1:p.Arg156Ser	NP_001381659.1:p.Arg156Cys

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#.

55 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	APPLERA_GI	ss48408949	Mar 14, 2006 (126)
2	SEATTLESEQ	ss159704261	Dec 01, 2009 (131)
3	1000GENOMES	ss219916094	Jul 14, 2010 (132)
4	NHLBI-ESP	ss342109101	May 09, 2011 (134)
5	1000GENOMES	ss489861082	May 04, 2012 (137)
6	EXOME_CHIP	ss491334341	May 04, 2012 (137)
7	CLINSEQ_SNP	ss491803840	May 04, 2012 (137)
8	EVA-GONL	ss978150572	Aug 21, 2014 (142)
9	JMKIDD_LAB	ss1067447305	Aug 21, 2014 (142)
10	JMKIDD_LAB	ss1070082081	Aug 21, 2014 (142)
11	1000GENOMES	ss1302359052	Aug 21, 2014 (142)
12	1000GENOMES	ss1302359053	Aug 21, 2014 (142)
13	EVA_DECODE	ss1587609861	Apr 01, 2015 (144)
14	EVA_UK10K_ALSPAC	ss1606181029	Apr 01, 2015 (144)
15	EVA_UK10K_TWINSUK	ss1649175062	Apr 01, 2015 (144)
16	EVA_EXAC	ss1686824404	Apr 01, 2015 (144)
17	EVA_EXAC	ss1686824405	Apr 01, 2015 (144)
18	WEILL_CORNELL_DGM	ss1921400514	Feb 12, 2016 (147)
19	JJLAB	ss2021248990	Sep 14, 2016 (149)
20	USC_VALOUEV	ss2149316810	Dec 20, 2016 (150)
21	HUMAN_LONGEVITY	ss2240618113	Dec 20, 2016 (150)
22	GNOMAD	ss2733471523	Nov 08, 2017 (151)
23	GNOMAD	ss2746923711	Nov 08, 2017 (151)
24	GNOMAD	ss2788317955	Nov 08, 2017 (151)
25	AFFY	ss2985205957	Nov 08, 2017 (151)
26	SWEGEN	ss2991648490	Nov 08, 2017 (151)
27	CSHL	ss3344826939	Nov 08, 2017 (151)
28	ILLUMINA	ss3653974106	Oct 11, 2018 (152)
29	EGCUT_WGS	ss3659547806	Jul 13, 2019 (153)
30	EVA_DECODE	ss3706379151	Jul 13, 2019 (153)
31	ACPOP	ss3729532190	Jul 13, 2019 (153)
32	PACBIO	ss3784202123	Jul 13, 2019 (153)
33	PACBIO	ss3789733736	Jul 13, 2019 (153)
34	PACBIO	ss3794607344	Jul 13, 2019 (153)
35	KHV_HUMAN_GENOMES	ss3802669991	Jul 13, 2019 (153)
36	EVA	ss3823874416	Apr 25, 2020 (154)
37	EVA	ss3825623957	Apr 25, 2020 (154)
38	EVA	ss3827600856	Apr 25, 2020 (154)
39	SGDP_PRJ	ss3854976760	Apr 25, 2020 (154)
40	KRGDB	ss3900735483	Apr 25, 2020 (154)
41	FSA-LAB	ss3984209043	Apr 27, 2021 (155)
42	FSA-LAB	ss3984209044	Apr 27, 2021 (155)
43	EVA	ss3986223418	Apr 27, 2021 (155)
44	TOPMED	ss4550623856	Apr 27, 2021 (155)
45	TOPMED	ss4550623857	Apr 27, 2021 (155)
46	1000G_HIGH_COVERAGE	ss5252660808	Oct 13, 2022 (156)
47	1000G_HIGH_COVERAGE	ss5252660809	Oct 13, 2022 (156)
48	HUGCELL_USP	ss5452209557	Oct 13, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5530306423	Oct 13, 2022 (156)
50	SANFORD_IMAGENETICS	ss5631311934	Oct 13, 2022 (156)
51	EVA	ss5800103551	Oct 13, 2022 (156)
52	EVA	ss5821840656	Oct 13, 2022 (156)
53	EVA	ss5848540397	Oct 13, 2022 (156)
54	EVA	ss5935430816	Oct 13, 2022 (156)
55	EVA	ss5957582556	Oct 13, 2022 (156)
56	1000Genomes	NC_000002.11 - 241569742	Oct 11, 2018 (152)
57	1000Genomes_30x	NC_000002.12 - 240630325	Oct 13, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 241569742	Oct 11, 2018 (152)
59	Genetic variation in the Estonian population	NC_000002.11 - 241569742	Oct 11, 2018 (152)
60	ExAC Submission ignored due to conflicting rows: Row 6735567 (NC_000002.11:241569741:C:C 102818/105094, NC_000002.11:241569741:C:A 2276/105094) Row 6735568 (NC_000002.11:241569741:C:C 105085/105094, NC_000002.11:241569741:C:T 9/105094)	-	Oct 11, 2018 (152)
61	ExAC Submission ignored due to conflicting rows: Row 6735567 (NC_000002.11:241569741:C:C 102818/105094, NC_000002.11:241569741:C:A 2276/105094) Row 6735568 (NC_000002.11:241569741:C:C 105085/105094, NC_000002.11:241569741:C:T 9/105094)	-	Oct 11, 2018 (152)
62	gnomAD - Genomes Submission ignored due to conflicting rows: Row 95981762 (NC_000002.12:240630324:C:A 2902/140278) Row 95981763 (NC_000002.12:240630324:C:T 21/140286)	-	Apr 27, 2021 (155)
63	gnomAD - Genomes Submission ignored due to conflicting rows: Row 95981762 (NC_000002.12:240630324:C:A 2902/140278) Row 95981763 (NC_000002.12:240630324:C:T 21/140286)	-	Apr 27, 2021 (155)
64	gnomAD - Exomes Submission ignored due to conflicting rows: Row 2541133 (NC_000002.11:241569741:C:C 224176/228666, NC_000002.11:241569741:C:A 4490/228666) Row 2541134 (NC_000002.11:241569741:C:C 228645/228666, NC_000002.11:241569741:C:T 21/228666)	-	Jul 13, 2019 (153)
65	gnomAD - Exomes Submission ignored due to conflicting rows: Row 2541133 (NC_000002.11:241569741:C:C 224176/228666, NC_000002.11:241569741:C:A 4490/228666) Row 2541134 (NC_000002.11:241569741:C:C 228645/228666, NC_000002.11:241569741:C:T 21/228666)	-	Jul 13, 2019 (153)
66	GO Exome Sequencing Project	NC_000002.11 - 241569742	Oct 11, 2018 (152)
67	KOREAN population from KRGDB	NC_000002.11 - 241569742	Apr 25, 2020 (154)
68	Northern Sweden	NC_000002.11 - 241569742	Jul 13, 2019 (153)
69	Qatari	NC_000002.11 - 241569742	Apr 25, 2020 (154)
70	SGDP_PRJ	NC_000002.11 - 241569742	Apr 25, 2020 (154)
71	Siberian	NC_000002.11 - 241569742	Apr 25, 2020 (154)
72	TopMed Submission ignored due to conflicting rows: Row 354446735 (NC_000002.12:240630324:C:A 5147/264690) Row 354446736 (NC_000002.12:240630324:C:T 39/264690)	-	Apr 27, 2021 (155)
73	TopMed Submission ignored due to conflicting rows: Row 354446735 (NC_000002.12:240630324:C:A 5147/264690) Row 354446736 (NC_000002.12:240630324:C:T 39/264690)	-	Apr 27, 2021 (155)
74	UK 10K study - Twins	NC_000002.11 - 241569742	Oct 11, 2018 (152)
75	ALFA	NC_000002.12 - 240630325	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
ss491803840, ss1587609861	NC_000002.10:241218414:C:A	NC_000002.12:240630324:C:A	(self)
13489697, 7477587, 5286054, 332811, 7912877, 2817055, 3442444, 6993740, 1833164, 7477587, ss219916094, ss342109101, ss489861082, ss491334341, ss978150572, ss1067447305, ss1070082081, ss1302359052, ss1606181029, ss1649175062, ss1686824404, ss1921400514, ss2021248990, ss2149316810, ss2733471523, ss2746923711, ss2788317955, ss2985205957, ss2991648490, ss3344826939, ss3653974106, ss3659547806, ss3729532190, ss3784202123, ss3789733736, ss3794607344, ss3823874416, ss3825623957, ss3827600856, ss3854976760, ss3900735483, ss3984209043, ss3984209044, ss3986223418, ss5631311934, ss5800103551, ss5821840656, ss5848540397, ss5957582556	NC_000002.11:241569741:C:A	NC_000002.12:240630324:C:A	(self)
17832358, 9429370498, ss2240618113, ss3706379151, ss3802669991, ss4550623856, ss5252660809, ss5452209557, ss5530306423, ss5935430816	NC_000002.12:240630324:C:A	NC_000002.12:240630324:C:A	(self)
ss48408949, ss159704261	NT_005416.13:760609:C:A	NC_000002.12:240630324:C:A	(self)
13489697, ss1302359053, ss1686824405, ss2733471523, ss2746923711, ss2788317955, ss5631311934	NC_000002.11:241569741:C:T	NC_000002.12:240630324:C:T	(self)
17832358, 9429370498, ss2240618113, ss4550623857, ss5252660808, ss5530306423	NC_000002.12:240630324:C:T	NC_000002.12:240630324: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 rs34778053

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs34778053