Name: rs1409817
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.

rs1409817

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr20:21400310 (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>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.129378 (34245/264690, TOPMED)
C=0.136992 (19189/140074, GnomAD)
C=0.01462 (245/16760, 8.3KJPN) (+ 14 more)
C=0.18874 (2930/15524, ALFA)
C=0.0809 (518/6404, 1000G_30x)
C=0.0795 (398/5008, 1000G)
C=0.2016 (903/4480, Estonian)
C=0.1915 (738/3854, ALSPAC)
C=0.1688 (626/3708, TWINSUK)
C=0.0133 (39/2930, KOREAN)
C=0.0153 (28/1832, Korea1K)
C=0.184 (184/998, GoNL)
C=0.203 (122/600, NorthernSweden)
C=0.104 (57/550, SGDP_PRJ)
C=0.111 (24/216, Qatari)
C=0.12 (7/56, Siberian)
C=0.17 (7/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: LOC105372558 : 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	15524	C=0.18874	A=0.81126
European	Sub	10628	C=0.20879	A=0.79121
African	Sub	1696	C=0.0678	A=0.9322
African Others	Sub	58	C=0.00	A=1.00
African American	Sub	1638	C=0.0702	A=0.9298
Asian	Sub	38	C=0.00	A=1.00
East Asian	Sub	30	C=0.00	A=1.00
Other Asian	Sub	8	C=0.0	A=1.0
Latin American 1	Sub	336	C=0.173	A=0.827
Latin American 2	Sub	72	C=0.38	A=0.62
South Asian	Sub	48	C=0.08	A=0.92
Other	Sub	2706	C=0.1874	A=0.8126

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=0.129378	A=0.870622
gnomAD - Genomes	Global	Study-wide	140074	C=0.136992	A=0.863008
gnomAD - Genomes	European	Sub	75836	C=0.18722	A=0.81278
gnomAD - Genomes	African	Sub	41998	C=0.05612	A=0.94388
gnomAD - Genomes	American	Sub	13634	C=0.14706	A=0.85294
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.0921	A=0.9079
gnomAD - Genomes	East Asian	Sub	3134	C=0.0147	A=0.9853
gnomAD - Genomes	Other	Sub	2148	C=0.1290	A=0.8710
8.3KJPN	JAPANESE	Study-wide	16760	C=0.01462	A=0.98538
Allele Frequency Aggregator	Total	Global	15524	C=0.18874	A=0.81126
Allele Frequency Aggregator	European	Sub	10628	C=0.20879	A=0.79121
Allele Frequency Aggregator	Other	Sub	2706	C=0.1874	A=0.8126
Allele Frequency Aggregator	African	Sub	1696	C=0.0678	A=0.9322
Allele Frequency Aggregator	Latin American 1	Sub	336	C=0.173	A=0.827
Allele Frequency Aggregator	Latin American 2	Sub	72	C=0.38	A=0.62
Allele Frequency Aggregator	South Asian	Sub	48	C=0.08	A=0.92
Allele Frequency Aggregator	Asian	Sub	38	C=0.00	A=1.00
1000Genomes_30x	Global	Study-wide	6404	C=0.0809	A=0.9191
1000Genomes_30x	African	Sub	1786	C=0.0336	A=0.9664
1000Genomes_30x	Europe	Sub	1266	C=0.1746	A=0.8254
1000Genomes_30x	South Asian	Sub	1202	C=0.0740	A=0.9260
1000Genomes_30x	East Asian	Sub	1170	C=0.0145	A=0.9855
1000Genomes_30x	American	Sub	980	C=0.134	A=0.866
1000Genomes	Global	Study-wide	5008	C=0.0795	A=0.9205
1000Genomes	African	Sub	1322	C=0.0378	A=0.9622
1000Genomes	East Asian	Sub	1008	C=0.0159	A=0.9841
1000Genomes	Europe	Sub	1006	C=0.1750	A=0.8250
1000Genomes	South Asian	Sub	978	C=0.067	A=0.933
1000Genomes	American	Sub	694	C=0.130	A=0.870
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.2016	A=0.7984
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.1915	A=0.8085
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.1688	A=0.8312
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0133	A=0.9867, G=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	C=0.0153	A=0.9847
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.184	A=0.816
Northern Sweden	ACPOP	Study-wide	600	C=0.203	A=0.797
SGDP_PRJ	Global	Study-wide	550	C=0.104	A=0.896
Qatari	Global	Study-wide	216	C=0.111	A=0.889
Siberian	Global	Study-wide	56	C=0.12	A=0.88
The Danish reference pan genome	Danish	Study-wide	40	C=0.17	A=0.82

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 20	NC_000020.11:g.21400310C>A
GRCh38.p14 chr 20	NC_000020.11:g.21400310C>G
GRCh38.p14 chr 20	NC_000020.11:g.21400310C>T
GRCh37.p13 chr 20	NC_000020.10:g.21380948C>A
GRCh37.p13 chr 20	NC_000020.10:g.21380948C>G
GRCh37.p13 chr 20	NC_000020.10:g.21380948C>T

Gene: LOC105372558, uncharacterized LOC105372558 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
LOC105372558 transcript variant X1	XR_001754526.1:n.	N/A	Intron Variant
LOC105372558 transcript variant X2	XR_001754528.1:n.	N/A	Intron Variant
LOC105372558 transcript variant X3	XR_001754530.1:n.	N/A	Intron Variant
LOC105372558 transcript variant X7	XR_001754527.3:n.	N/A	Genic Downstream Transcript Variant
LOC105372558 transcript variant X8	XR_001754531.3:n.	N/A	Genic Downstream Transcript Variant
LOC105372558 transcript variant X4	XR_001754532.1:n.	N/A	Genic Downstream Transcript Variant
LOC105372558 transcript variant X5	XR_007067725.1:n.	N/A	Genic Downstream Transcript Variant
LOC105372558 transcript variant X6	XR_937325.4:n.	N/A	Genic Downstream Transcript Variant
LOC105372558 transcript variant X9	XR_937329.4:n.	N/A	Genic Downstream Transcript Variant
LOC105372558 transcript variant X10	XR_937330.4:n.	N/A	Genic Downstream 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	G	T
GRCh38.p14 chr 20	NC_000020.11:g.21400310=	NC_000020.11:g.21400310C>A	NC_000020.11:g.21400310C>G	NC_000020.11:g.21400310C>T
GRCh37.p13 chr 20	NC_000020.10:g.21380948=	NC_000020.10:g.21380948C>A	NC_000020.10:g.21380948C>G	NC_000020.10:g.21380948C>T

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#.

78 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss2210467	Oct 23, 2000 (88)
2	SC_SNP	ss8358598	Apr 21, 2003 (114)
3	WI_SSAHASNP	ss12490821	Jul 11, 2003 (116)
4	CSHL-HAPMAP	ss19478097	Feb 27, 2004 (120)
5	SSAHASNP	ss21783986	Apr 05, 2004 (123)
6	BCMHGSC_JDW	ss91665911	Mar 24, 2008 (129)
7	HUMANGENOME_JCVI	ss96190773	Feb 04, 2009 (130)
8	BGI	ss106182882	Feb 04, 2009 (130)
9	1000GENOMES	ss111856730	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss117511877	Feb 14, 2009 (130)
11	ENSEMBL	ss135744081	Dec 01, 2009 (131)
12	GMI	ss156265582	Dec 01, 2009 (131)
13	COMPLETE_GENOMICS	ss169326103	Jul 04, 2010 (132)
14	COMPLETE_GENOMICS	ss171995990	Jul 04, 2010 (132)
15	BUSHMAN	ss203856030	Jul 04, 2010 (132)
16	BCM-HGSC-SUB	ss208697338	Jul 04, 2010 (132)
17	1000GENOMES	ss212010221	Jul 14, 2010 (132)
18	1000GENOMES	ss228301929	Jul 14, 2010 (132)
19	1000GENOMES	ss237796989	Jul 15, 2010 (132)
20	1000GENOMES	ss243976235	Jul 15, 2010 (132)
21	BL	ss255539239	May 09, 2011 (134)
22	GMI	ss283332318	May 04, 2012 (137)
23	GMI	ss287437232	Apr 25, 2013 (138)
24	PJP	ss292629863	May 09, 2011 (134)
25	ILLUMINA	ss480614568	Sep 08, 2015 (146)
26	TISHKOFF	ss566188462	Apr 25, 2013 (138)
27	SSMP	ss662063607	Apr 25, 2013 (138)
28	EVA-GONL	ss994626056	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1082138105	Aug 21, 2014 (142)
30	1000GENOMES	ss1364380421	Aug 21, 2014 (142)
31	DDI	ss1429021790	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1579472543	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1638585216	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1681579249	Apr 01, 2015 (144)
35	EVA_DECODE	ss1698684941	Apr 01, 2015 (144)
36	HAMMER_LAB	ss1809459108	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1938133011	Feb 12, 2016 (147)
38	GENOMED	ss1969112592	Jul 19, 2016 (147)
39	JJLAB	ss2029851769	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2158404593	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2241985065	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2629421134	Nov 08, 2017 (151)
43	GRF	ss2704080561	Nov 08, 2017 (151)
44	GNOMAD	ss2966314605	Nov 08, 2017 (151)
45	SWEGEN	ss3017995288	Nov 08, 2017 (151)
46	BIOINF_KMB_FNS_UNIBA	ss3028759161	Nov 08, 2017 (151)
47	CSHL	ss3352458196	Nov 08, 2017 (151)
48	ILLUMINA	ss3636521895	Oct 12, 2018 (152)
49	URBANLAB	ss3650989673	Oct 12, 2018 (152)
50	EGCUT_WGS	ss3684720374	Jul 13, 2019 (153)
51	EVA_DECODE	ss3706717446	Jul 13, 2019 (153)
52	ACPOP	ss3743319925	Jul 13, 2019 (153)
53	EVA	ss3758524276	Jul 13, 2019 (153)
54	PACBIO	ss3788621376	Jul 13, 2019 (153)
55	PACBIO	ss3793518550	Jul 13, 2019 (153)
56	PACBIO	ss3798405729	Jul 13, 2019 (153)
57	KHV_HUMAN_GENOMES	ss3821692726	Jul 13, 2019 (153)
58	EVA	ss3835629961	Apr 27, 2020 (154)
59	EVA	ss3841441223	Apr 27, 2020 (154)
60	EVA	ss3846949357	Apr 27, 2020 (154)
61	SGDP_PRJ	ss3888897743	Apr 27, 2020 (154)
62	KRGDB	ss3939102681	Apr 27, 2020 (154)
63	KOGIC	ss3981969958	Apr 27, 2020 (154)
64	TOPMED	ss5085023636	Apr 26, 2021 (155)
65	TOMMO_GENOMICS	ss5229192535	Apr 26, 2021 (155)
66	1000G_HIGH_COVERAGE	ss5308358183	Oct 13, 2022 (156)
67	EVA	ss5436770259	Oct 13, 2022 (156)
68	HUGCELL_USP	ss5500736125	Oct 13, 2022 (156)
69	EVA	ss5512182997	Oct 13, 2022 (156)
70	1000G_HIGH_COVERAGE	ss5614579394	Oct 13, 2022 (156)
71	SANFORD_IMAGENETICS	ss5663022442	Oct 13, 2022 (156)
72	TOMMO_GENOMICS	ss5788278941	Oct 13, 2022 (156)
73	TOMMO_GENOMICS	ss5788278942	Oct 13, 2022 (156)
74	YY_MCH	ss5817886679	Oct 13, 2022 (156)
75	EVA	ss5845555630	Oct 13, 2022 (156)
76	EVA	ss5853104171	Oct 13, 2022 (156)
77	EVA	ss5922995016	Oct 13, 2022 (156)
78	EVA	ss5957936527	Oct 13, 2022 (156)
79	1000Genomes	NC_000020.10 - 21380948	Oct 12, 2018 (152)
80	1000Genomes_30x	NC_000020.11 - 21400310	Oct 13, 2022 (156)
81	The Avon Longitudinal Study of Parents and Children	NC_000020.10 - 21380948	Oct 12, 2018 (152)
82	Genetic variation in the Estonian population	NC_000020.10 - 21380948	Oct 12, 2018 (152)
83	The Danish reference pan genome	NC_000020.10 - 21380948	Apr 27, 2020 (154)
84	gnomAD - Genomes	NC_000020.11 - 21400310	Apr 26, 2021 (155)
85	Genome of the Netherlands Release 5	NC_000020.10 - 21380948	Apr 27, 2020 (154)
86	KOREAN population from KRGDB	NC_000020.10 - 21380948	Apr 27, 2020 (154)
87	Korean Genome Project	NC_000020.11 - 21400310	Apr 27, 2020 (154)
88	Northern Sweden	NC_000020.10 - 21380948	Jul 13, 2019 (153)
89	Qatari	NC_000020.10 - 21380948	Apr 27, 2020 (154)
90	SGDP_PRJ	NC_000020.10 - 21380948	Apr 27, 2020 (154)
91	Siberian	NC_000020.10 - 21380948	Apr 27, 2020 (154)
92	8.3KJPN	NC_000020.10 - 21380948	Apr 26, 2021 (155)
93	14KJPN Submission ignored due to conflicting rows: Row 122116045 (NC_000020.11:21400309:C:A 27845/28258) Row 122116046 (NC_000020.11:21400309:C:T 3/28258)	-	Oct 13, 2022 (156)
94	14KJPN Submission ignored due to conflicting rows: Row 122116045 (NC_000020.11:21400309:C:A 27845/28258) Row 122116046 (NC_000020.11:21400309:C:T 3/28258)	-	Oct 13, 2022 (156)
95	TopMed	NC_000020.11 - 21400310	Apr 26, 2021 (155)
96	UK 10K study - Twins	NC_000020.10 - 21380948	Oct 12, 2018 (152)
97	ALFA	NC_000020.11 - 21400310	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).

Associated ID	History Updated (Build)
rs13041966	Sep 24, 2004 (123)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss91665911, ss111856730, ss117511877, ss169326103, ss171995990, ss203856030, ss208697338, ss212010221, ss255539239, ss283332318, ss287437232, ss292629863, ss1698684941	NC_000020.9:21328947:C:A	NC_000020.11:21400309:C:A	(self)
77831101, 43094261, 30458622, 5637482, 19202567, 46280075, 16604790, 20174933, 40914723, 10920947, 87161842, 43094261, ss228301929, ss237796989, ss243976235, ss480614568, ss566188462, ss662063607, ss994626056, ss1082138105, ss1364380421, ss1429021790, ss1579472543, ss1638585216, ss1681579249, ss1809459108, ss1938133011, ss1969112592, ss2029851769, ss2158404593, ss2629421134, ss2704080561, ss2966314605, ss3017995288, ss3352458196, ss3636521895, ss3684720374, ss3743319925, ss3758524276, ss3788621376, ss3793518550, ss3798405729, ss3835629961, ss3841441223, ss3888897743, ss3939102681, ss5229192535, ss5436770259, ss5512182997, ss5663022442, ss5845555630, ss5957936527	NC_000020.10:21380947:C:A	NC_000020.11:21400309:C:A	(self)
102105329, 548731266, 38347959, 360132581, 3436993056, ss2241985065, ss3028759161, ss3650989673, ss3706717446, ss3821692726, ss3846949357, ss3981969958, ss5085023636, ss5308358183, ss5500736125, ss5614579394, ss5788278941, ss5817886679, ss5853104171, ss5922995016	NC_000020.11:21400309:C:A	NC_000020.11:21400309:C:A	(self)
ss2210467, ss8358598, ss12490821, ss19478097, ss21783986, ss96190773, ss106182882, ss135744081, ss156265582	NT_011387.8:21320947:C:A	NC_000020.11:21400309:C:A	(self)
46280075, ss3939102681	NC_000020.10:21380947:C:G	NC_000020.11:21400309:C:G	(self)
ss5788278942	NC_000020.11:21400309:C:T	NC_000020.11:21400309:C:T

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1409817

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

rs1409817