Name: rs114684774
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.

rs114684774

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:53112555 (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=0.00164 (32/19486, ALFA)
A=0.0100 (64/6404, 1000G_30x)
A=0.0108 (54/5008, 1000G) (+ 6 more)
A=0.0058 (26/4480, Estonian)
A=0.007 (7/998, GoNL)
A=0.007 (4/600, NorthernSweden)
A=0.005 (1/216, Qatari)
C=0.5 (3/6, SGDP_PRJ)
A=0.5 (3/6, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: SLC1A7 : 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	19486	C=0.99836	A=0.00164, T=0.00000
European	Sub	14046	C=0.99815	A=0.00185, T=0.00000
African	Sub	3378	C=0.9997	A=0.0003, T=0.0000
African Others	Sub	114	C=1.000	A=0.000, T=0.000
African American	Sub	3264	C=0.9997	A=0.0003, T=0.0000
Asian	Sub	116	C=1.000	A=0.000, T=0.000
East Asian	Sub	88	C=1.00	A=0.00, T=0.00
Other Asian	Sub	28	C=1.00	A=0.00, T=0.00
Latin American 1	Sub	150	C=1.000	A=0.000, T=0.000
Latin American 2	Sub	610	C=1.000	A=0.000, T=0.000
South Asian	Sub	94	C=1.00	A=0.00, T=0.00
Other	Sub	1092	C=0.9954	A=0.0046, 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	19486	C=0.99836	A=0.00164, T=0.00000
Allele Frequency Aggregator	European	Sub	14046	C=0.99815	A=0.00185, T=0.00000
Allele Frequency Aggregator	African	Sub	3378	C=0.9997	A=0.0003, T=0.0000
Allele Frequency Aggregator	Other	Sub	1092	C=0.9954	A=0.0046, T=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	150	C=1.000	A=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	116	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
1000Genomes_30x	Global	Study-wide	6404	C=0.9900	A=0.0100
1000Genomes_30x	African	Sub	1786	C=0.9994	A=0.0006
1000Genomes_30x	Europe	Sub	1266	C=0.9889	A=0.0111
1000Genomes_30x	South Asian	Sub	1202	C=0.9651	A=0.0349
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	A=0.0000
1000Genomes_30x	American	Sub	980	C=0.993	A=0.007
1000Genomes	Global	Study-wide	5008	C=0.9892	A=0.0108
1000Genomes	African	Sub	1322	C=0.9992	A=0.0008
1000Genomes	East Asian	Sub	1008	C=1.0000	A=0.0000
1000Genomes	Europe	Sub	1006	C=0.9881	A=0.0119
1000Genomes	South Asian	Sub	978	C=0.964	A=0.036
1000Genomes	American	Sub	694	C=0.991	A=0.009
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9942	A=0.0058
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.993	A=0.007
Northern Sweden	ACPOP	Study-wide	600	C=0.993	A=0.007
Qatari	Global	Study-wide	216	C=0.995	A=0.005
SGDP_PRJ	Global	Study-wide	6	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 1	NC_000001.11:g.53112555C>A
GRCh38.p14 chr 1	NC_000001.11:g.53112555C>T
GRCh37.p13 chr 1	NC_000001.10:g.53578227C>A
GRCh37.p13 chr 1	NC_000001.10:g.53578227C>T

Gene: SLC1A7, solute carrier family 1 member 7 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SLC1A7 transcript variant 1	NM_001287595.2:c.431+2203… NM_001287595.2:c.431+2203G>T	N/A	Intron Variant
SLC1A7 transcript variant 2	NM_001287596.2:c.431+2203… NM_001287596.2:c.431+2203G>T	N/A	Intron Variant
SLC1A7 transcript variant 3	NM_001287597.2:c.216-6781… NM_001287597.2:c.216-6781G>T	N/A	Intron Variant
SLC1A7 transcript variant 4	NM_006671.6:c.431+2203G>T	N/A	Intron Variant
SLC1A7 transcript variant 5	NR_109858.2:n.	N/A	Intron Variant
SLC1A7 transcript variant X2	XM_011542002.3:c.	N/A	Genic Upstream Transcript Variant
SLC1A7 transcript variant X1	XM_047428531.1:c.	N/A	Genic Upstream Transcript 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 1	NC_000001.11:g.53112555=	NC_000001.11:g.53112555C>A	NC_000001.11:g.53112555C>T
GRCh37.p13 chr 1	NC_000001.10:g.53578227=	NC_000001.10:g.53578227C>A	NC_000001.10:g.53578227C>T
SLC1A7 transcript variant 1	NM_001287595.2:c.431+2203=	NM_001287595.2:c.431+2203G>T	NM_001287595.2:c.431+2203G>A
SLC1A7 transcript variant 2	NM_001287596.2:c.431+2203=	NM_001287596.2:c.431+2203G>T	NM_001287596.2:c.431+2203G>A
SLC1A7 transcript variant 3	NM_001287597.2:c.216-6781=	NM_001287597.2:c.216-6781G>T	NM_001287597.2:c.216-6781G>A
SLC1A7 transcript	NM_006671.4:c.431+2203=	NM_006671.4:c.431+2203G>T	NM_006671.4:c.431+2203G>A
SLC1A7 transcript variant 4	NM_006671.6:c.431+2203=	NM_006671.6:c.431+2203G>T	NM_006671.6:c.431+2203G>A
SLC1A7 transcript variant X1	XM_005271133.1:c.431+2203=	XM_005271133.1:c.431+2203G>T	XM_005271133.1:c.431+2203G>A
SLC1A7 transcript variant X2	XM_005271134.1:c.216-6781=	XM_005271134.1:c.216-6781G>T	XM_005271134.1:c.216-6781G>A

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, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss230528915	Jul 14, 2010 (132)
2	ILLUMINA	ss535706051	Sep 08, 2015 (146)
3	SSMP	ss647920399	Apr 25, 2013 (138)
4	EVA-GONL	ss975146272	Aug 21, 2014 (142)
5	JMKIDD_LAB	ss1067875362	Aug 21, 2014 (142)
6	1000GENOMES	ss1290838556	Aug 21, 2014 (142)
7	EVA_DECODE	ss1584512017	Apr 01, 2015 (144)
8	EVA_UK10K_ALSPAC	ss1600144862	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1600144863	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1643138895	Apr 01, 2015 (144)
11	EVA_UK10K_TWINSUK	ss1643138896	Apr 01, 2015 (144)
12	WEILL_CORNELL_DGM	ss1918354882	Feb 12, 2016 (147)
13	HUMAN_LONGEVITY	ss2162394211	Dec 20, 2016 (150)
14	GNOMAD	ss2755004132	Nov 08, 2017 (151)
15	SWEGEN	ss2986795456	Nov 08, 2017 (151)
16	ILLUMINA	ss3021086391	Nov 08, 2017 (151)
17	CSHL	ss3343447405	Nov 08, 2017 (151)
18	ILLUMINA	ss3626094044	Oct 11, 2018 (152)
19	ILLUMINA	ss3651412682	Oct 11, 2018 (152)
20	EGCUT_WGS	ss3654858622	Jul 12, 2019 (153)
21	EVA_DECODE	ss3686744552	Jul 12, 2019 (153)
22	ILLUMINA	ss3725023413	Jul 12, 2019 (153)
23	ACPOP	ss3727034832	Jul 12, 2019 (153)
24	SGDP_PRJ	ss3848818064	Apr 25, 2020 (154)
25	TOPMED	ss4449290380	Apr 25, 2021 (155)
26	TOPMED	ss4449290381	Apr 25, 2021 (155)
27	TOMMO_GENOMICS	ss5143890199	Apr 25, 2021 (155)
28	TOMMO_GENOMICS	ss5143890200	Apr 25, 2021 (155)
29	1000G_HIGH_COVERAGE	ss5242222814	Oct 17, 2022 (156)
30	EVA	ss5318637358	Oct 17, 2022 (156)
31	HUGCELL_USP	ss5443288773	Oct 17, 2022 (156)
32	1000G_HIGH_COVERAGE	ss5514476665	Oct 17, 2022 (156)
33	SANFORD_IMAGENETICS	ss5625502128	Oct 17, 2022 (156)
34	TOMMO_GENOMICS	ss5668645128	Oct 17, 2022 (156)
35	TOMMO_GENOMICS	ss5668645129	Oct 17, 2022 (156)
36	EVA	ss5831940443	Oct 17, 2022 (156)
37	EVA	ss5908204445	Oct 17, 2022 (156)
38	EVA	ss5937332559	Oct 17, 2022 (156)
39	1000Genomes	NC_000001.10 - 53578227	Oct 11, 2018 (152)
40	1000Genomes_30x	NC_000001.11 - 53112555	Oct 17, 2022 (156)
41	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 845082 (NC_000001.10:53578226:C:C 3820/3854, NC_000001.10:53578226:C:A 34/3854) Row 845083 (NC_000001.10:53578226:C:C 3853/3854, NC_000001.10:53578226:C:T 1/3854)	-	Oct 11, 2018 (152)
42	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 845082 (NC_000001.10:53578226:C:C 3820/3854, NC_000001.10:53578226:C:A 34/3854) Row 845083 (NC_000001.10:53578226:C:C 3853/3854, NC_000001.10:53578226:C:T 1/3854)	-	Oct 11, 2018 (152)
43	Genetic variation in the Estonian population	NC_000001.10 - 53578227	Oct 11, 2018 (152)
44	gnomAD - Genomes Submission ignored due to conflicting rows: Row 11025764 (NC_000001.11:53112554:C:A 1203/140264) Row 11025765 (NC_000001.11:53112554:C:T 5/140266)	-	Apr 25, 2021 (155)
45	gnomAD - Genomes Submission ignored due to conflicting rows: Row 11025764 (NC_000001.11:53112554:C:A 1203/140264) Row 11025765 (NC_000001.11:53112554:C:T 5/140266)	-	Apr 25, 2021 (155)
46	Genome of the Netherlands Release 5	NC_000001.10 - 53578227	Apr 25, 2020 (154)
47	Northern Sweden	NC_000001.10 - 53578227	Jul 12, 2019 (153)
48	Qatari	NC_000001.10 - 53578227	Apr 25, 2020 (154)
49	SGDP_PRJ	NC_000001.10 - 53578227	Apr 25, 2020 (154)
50	8.3KJPN Submission ignored due to conflicting rows: Row 1859506 (NC_000001.10:53578226:C:T 4/16760) Row 1859507 (NC_000001.10:53578226:C:A 1/16760)	-	Apr 25, 2021 (155)
51	8.3KJPN Submission ignored due to conflicting rows: Row 1859506 (NC_000001.10:53578226:C:T 4/16760) Row 1859507 (NC_000001.10:53578226:C:A 1/16760)	-	Apr 25, 2021 (155)
52	14KJPN Submission ignored due to conflicting rows: Row 2482232 (NC_000001.11:53112554:C:T 8/28258) Row 2482233 (NC_000001.11:53112554:C:A 1/28258)	-	Oct 17, 2022 (156)
53	14KJPN Submission ignored due to conflicting rows: Row 2482232 (NC_000001.11:53112554:C:T 8/28258) Row 2482233 (NC_000001.11:53112554:C:A 1/28258)	-	Oct 17, 2022 (156)
54	TopMed Submission ignored due to conflicting rows: Row 12896715 (NC_000001.11:53112554:C:A 2450/264690) Row 12896716 (NC_000001.11:53112554:C:T 9/264690)	-	Apr 25, 2021 (155)
55	TopMed Submission ignored due to conflicting rows: Row 12896715 (NC_000001.11:53112554:C:A 2450/264690) Row 12896716 (NC_000001.11:53112554:C:T 9/264690)	-	Apr 25, 2021 (155)
56	UK 10K study - Twins Submission ignored due to conflicting rows: Row 845082 (NC_000001.10:53578226:C:C 3677/3708, NC_000001.10:53578226:C:A 31/3708) Row 845083 (NC_000001.10:53578226:C:C 3708/3708, NC_000001.10:53578226:C:T 0/3708)	-	Oct 11, 2018 (152)
57	UK 10K study - Twins Submission ignored due to conflicting rows: Row 845082 (NC_000001.10:53578226:C:C 3677/3708, NC_000001.10:53578226:C:A 31/3708) Row 845083 (NC_000001.10:53578226:C:C 3708/3708, NC_000001.10:53578226:C:T 0/3708)	-	Oct 11, 2018 (152)
58	ALFA	NC_000001.11 - 53112555	Apr 25, 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
ss1584512017	NC_000001.9:53350814:C:A	NC_000001.11:53112554:C:A	(self)
1555053, 596870, 358164, 319697, 396812, 835044, ss230528915, ss535706051, ss647920399, ss975146272, ss1067875362, ss1290838556, ss1600144862, ss1643138895, ss1918354882, ss2755004132, ss2986795456, ss3021086391, ss3343447405, ss3626094044, ss3651412682, ss3654858622, ss3727034832, ss3848818064, ss5143890200, ss5318637358, ss5625502128, ss5831940443, ss5937332559	NC_000001.10:53578226:C:A	NC_000001.11:53112554:C:A	(self)
2002600, 3997220624, ss2162394211, ss3686744552, ss3725023413, ss4449290380, ss5242222814, ss5443288773, ss5514476665, ss5668645129, ss5908204445	NC_000001.11:53112554:C:A	NC_000001.11:53112554:C:A	(self)
ss1600144863, ss1643138896, ss5143890199	NC_000001.10:53578226:C:T	NC_000001.11:53112554:C:T	(self)
3997220624, ss2162394211, ss4449290381, ss5668645128	NC_000001.11:53112554:C:T	NC_000001.11:53112554: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 rs114684774

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

rs114684774