Name: rs893306
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.

rs893306

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr8:28556431 (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: T>A / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.416317 (110195/264690, TOPMED)
T=0.417291 (58399/139948, GnomAD)
T=0.39805 (11248/28258, 14KJPN) (+ 17 more)
T=0.42494 (7632/17960, ALFA)
T=0.39481 (6617/16760, 8.3KJPN)
T=0.3876 (2482/6404, 1000G_30x)
T=0.3844 (1925/5008, 1000G)
T=0.4087 (1831/4480, Estonian)
T=0.4424 (1705/3854, ALSPAC)
T=0.4426 (1641/3708, TWINSUK)
T=0.3515 (1030/2930, KOREAN)
T=0.3384 (620/1832, Korea1K)
T=0.464 (463/998, GoNL)
T=0.475 (285/600, NorthernSweden)
T=0.252 (116/460, SGDP_PRJ)
T=0.430 (141/328, HapMap)
T=0.306 (66/216, Qatari)
T=0.304 (65/214, Vietnamese)
T=0.20 (9/46, Siberian)
G=0.47 (19/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FZD3 : 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	17960	T=0.42494	A=0.00000, G=0.57506
European	Sub	13760	T=0.42703	A=0.00000, G=0.57297
African	Sub	2546	T=0.4340	A=0.0000, G=0.5660
African Others	Sub	100	T=0.50	A=0.00, G=0.50
African American	Sub	2446	T=0.4313	A=0.0000, G=0.5687
Asian	Sub	112	T=0.348	A=0.000, G=0.652
East Asian	Sub	86	T=0.36	A=0.00, G=0.64
Other Asian	Sub	26	T=0.31	A=0.00, G=0.69
Latin American 1	Sub	146	T=0.404	A=0.000, G=0.596
Latin American 2	Sub	610	T=0.403	A=0.000, G=0.597
South Asian	Sub	98	T=0.34	A=0.00, G=0.66
Other	Sub	688	T=0.398	A=0.000, G=0.602

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	T=0.416317	G=0.583683
gnomAD - Genomes	Global	Study-wide	139948	T=0.417291	G=0.582709
gnomAD - Genomes	European	Sub	75818	T=0.42651	G=0.57349
gnomAD - Genomes	African	Sub	41902	T=0.41451	G=0.58549
gnomAD - Genomes	American	Sub	13628	T=0.40586	G=0.59414
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.3575	G=0.6425
gnomAD - Genomes	East Asian	Sub	3130	T=0.3473	G=0.6527
gnomAD - Genomes	Other	Sub	2150	T=0.4130	G=0.5870
14KJPN	JAPANESE	Study-wide	28258	T=0.39805	G=0.60195
Allele Frequency Aggregator	Total	Global	17960	T=0.42494	A=0.00000, G=0.57506
Allele Frequency Aggregator	European	Sub	13760	T=0.42703	A=0.00000, G=0.57297
Allele Frequency Aggregator	African	Sub	2546	T=0.4340	A=0.0000, G=0.5660
Allele Frequency Aggregator	Other	Sub	688	T=0.398	A=0.000, G=0.602
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.403	A=0.000, G=0.597
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.404	A=0.000, G=0.596
Allele Frequency Aggregator	Asian	Sub	112	T=0.348	A=0.000, G=0.652
Allele Frequency Aggregator	South Asian	Sub	98	T=0.34	A=0.00, G=0.66
8.3KJPN	JAPANESE	Study-wide	16760	T=0.39481	G=0.60519
1000Genomes_30x	Global	Study-wide	6404	T=0.3876	G=0.6124
1000Genomes_30x	African	Sub	1786	T=0.4082	G=0.5918
1000Genomes_30x	Europe	Sub	1266	T=0.4131	G=0.5869
1000Genomes_30x	South Asian	Sub	1202	T=0.3719	G=0.6281
1000Genomes_30x	East Asian	Sub	1170	T=0.3521	G=0.6479
1000Genomes_30x	American	Sub	980	T=0.379	G=0.621
1000Genomes	Global	Study-wide	5008	T=0.3844	G=0.6156
1000Genomes	African	Sub	1322	T=0.4024	G=0.5976
1000Genomes	East Asian	Sub	1008	T=0.3472	G=0.6528
1000Genomes	Europe	Sub	1006	T=0.4066	G=0.5934
1000Genomes	South Asian	Sub	978	T=0.374	G=0.626
1000Genomes	American	Sub	694	T=0.386	G=0.614
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.4087	G=0.5913
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.4424	G=0.5576
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.4426	G=0.5574
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.3515	G=0.6485
Korean Genome Project	KOREAN	Study-wide	1832	T=0.3384	G=0.6616
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.464	G=0.536
Northern Sweden	ACPOP	Study-wide	600	T=0.475	G=0.525
SGDP_PRJ	Global	Study-wide	460	T=0.252	G=0.748
HapMap	Global	Study-wide	328	T=0.430	G=0.570
HapMap	American	Sub	120	T=0.392	G=0.608
HapMap	African	Sub	118	T=0.424	G=0.576
HapMap	Asian	Sub	90	T=0.49	G=0.51
Qatari	Global	Study-wide	216	T=0.306	G=0.694
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.304	G=0.696
Siberian	Global	Study-wide	46	T=0.20	G=0.80
The Danish reference pan genome	Danish	Study-wide	40	T=0.53	G=0.47

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 8	NC_000008.11:g.28556431T>A
GRCh38.p14 chr 8	NC_000008.11:g.28556431T>G
GRCh37.p13 chr 8	NC_000008.10:g.28413948T>A
GRCh37.p13 chr 8	NC_000008.10:g.28413948T>G
FZD3 RefSeqGene (LRG_859)	NG_029723.1:g.67227T>A
FZD3 RefSeqGene (LRG_859)	NG_029723.1:g.67227T>G

Gene: FZD3, frizzled class receptor 3 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FZD3 transcript variant 1	NM_017412.4:c.1787+460T>A	N/A	Intron Variant
FZD3 transcript variant 2	NM_145866.2:c.1787+460T>A	N/A	Intron Variant
FZD3 transcript variant X1	XM_017013841.2:c.1586+460… XM_017013841.2:c.1586+460T>A	N/A	Intron Variant
FZD3 transcript variant X3	XM_017013842.2:c.	N/A	Genic Downstream Transcript Variant
FZD3 transcript variant X4	XM_017013843.2:c.	N/A	Genic Downstream Transcript Variant
FZD3 transcript variant X5	XM_017013844.2:c.	N/A	Genic Downstream Transcript Variant
FZD3 transcript variant X2	XM_047422238.1:c.	N/A	Genic Downstream Transcript Variant
FZD3 transcript variant X6	XM_047422239.1:c.	N/A	Genic Downstream Transcript Variant
FZD3 transcript variant X7	XM_047422240.1:c.	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	T=	A	G
GRCh38.p14 chr 8	NC_000008.11:g.28556431=	NC_000008.11:g.28556431T>A	NC_000008.11:g.28556431T>G
GRCh37.p13 chr 8	NC_000008.10:g.28413948=	NC_000008.10:g.28413948T>A	NC_000008.10:g.28413948T>G
FZD3 RefSeqGene (LRG_859)	NG_029723.1:g.67227=	NG_029723.1:g.67227T>A	NG_029723.1:g.67227T>G
FZD3 transcript variant 1	NM_017412.3:c.1787+460=	NM_017412.3:c.1787+460T>A	NM_017412.3:c.1787+460T>G
FZD3 transcript variant 1	NM_017412.4:c.1787+460=	NM_017412.4:c.1787+460T>A	NM_017412.4:c.1787+460T>G
FZD3 transcript variant 2	NM_145866.1:c.1787+460=	NM_145866.1:c.1787+460T>A	NM_145866.1:c.1787+460T>G
FZD3 transcript variant 2	NM_145866.2:c.1787+460=	NM_145866.2:c.1787+460T>A	NM_145866.2:c.1787+460T>G
FZD3 transcript variant X1	XM_017013841.2:c.1586+460=	XM_017013841.2:c.1586+460T>A	XM_017013841.2:c.1586+460T>G

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#.

80 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1323082	Oct 05, 2000 (86)
2	TSC-CSHL	ss5490555	Oct 08, 2002 (108)
3	SC_JCM	ss5693416	Feb 20, 2003 (111)
4	CSHL-HAPMAP	ss17236531	Feb 27, 2004 (120)
5	SSAHASNP	ss22692294	Apr 05, 2004 (121)
6	ABI	ss43255696	Mar 14, 2006 (126)
7	HGSV	ss77583182	Dec 06, 2007 (129)
8	HGSV	ss80131256	Dec 15, 2007 (130)
9	HGSV	ss85550217	Dec 15, 2007 (130)
10	BCMHGSC_JDW	ss93862493	Mar 25, 2008 (129)
11	HUMANGENOME_JCVI	ss97862777	Feb 06, 2009 (130)
12	BGI	ss105609251	Feb 06, 2009 (130)
13	1000GENOMES	ss112946606	Jan 25, 2009 (130)
14	1000GENOMES	ss115198023	Jan 25, 2009 (130)
15	ILLUMINA-UK	ss115876921	Feb 14, 2009 (130)
16	ENSEMBL	ss134437374	Dec 01, 2009 (131)
17	ENSEMBL	ss143364026	Dec 01, 2009 (131)
18	GMI	ss156198724	Dec 01, 2009 (131)
19	COMPLETE_GENOMICS	ss164288650	Jul 04, 2010 (132)
20	COMPLETE_GENOMICS	ss166458330	Jul 04, 2010 (132)
21	BUSHMAN	ss198973475	Jul 04, 2010 (132)
22	BCM-HGSC-SUB	ss206475824	Jul 04, 2010 (132)
23	1000GENOMES	ss223624584	Jul 14, 2010 (132)
24	1000GENOMES	ss234380920	Jul 15, 2010 (132)
25	1000GENOMES	ss241249960	Jul 15, 2010 (132)
26	BL	ss254223814	May 09, 2011 (134)
27	GMI	ss279750899	May 04, 2012 (137)
28	GMI	ss285820169	Apr 25, 2013 (138)
29	PJP	ss294247828	May 09, 2011 (134)
30	TISHKOFF	ss560647441	Apr 25, 2013 (138)
31	SSMP	ss655081599	Apr 25, 2013 (138)
32	EVA-GONL	ss985344533	Aug 21, 2014 (142)
33	JMKIDD_LAB	ss1075394182	Aug 21, 2014 (142)
34	1000GENOMES	ss1329184899	Aug 21, 2014 (142)
35	DDI	ss1431464237	Apr 01, 2015 (144)
36	EVA_GENOME_DK	ss1582622782	Apr 01, 2015 (144)
37	EVA_DECODE	ss1594937874	Apr 01, 2015 (144)
38	EVA_UK10K_ALSPAC	ss1620281417	Apr 01, 2015 (144)
39	EVA_UK10K_TWINSUK	ss1663275450	Apr 01, 2015 (144)
40	HAMMER_LAB	ss1805465749	Sep 08, 2015 (146)
41	WEILL_CORNELL_DGM	ss1928634001	Feb 12, 2016 (147)
42	GENOMED	ss1970947126	Jul 19, 2016 (147)
43	JJLAB	ss2025019886	Sep 14, 2016 (149)
44	USC_VALOUEV	ss2153241930	Dec 20, 2016 (150)
45	HUMAN_LONGEVITY	ss2301849663	Dec 20, 2016 (150)
46	SYSTEMSBIOZJU	ss2626993751	Nov 08, 2017 (151)
47	GRF	ss2709004438	Nov 08, 2017 (151)
48	GNOMAD	ss2864842500	Nov 08, 2017 (151)
49	SWEGEN	ss3002911718	Nov 08, 2017 (151)
50	BIOINF_KMB_FNS_UNIBA	ss3026301287	Nov 08, 2017 (151)
51	CSHL	ss3348112881	Nov 08, 2017 (151)
52	URBANLAB	ss3648883753	Oct 12, 2018 (152)
53	EGCUT_WGS	ss3670596891	Jul 13, 2019 (153)
54	EVA_DECODE	ss3721693764	Jul 13, 2019 (153)
55	ACPOP	ss3735527269	Jul 13, 2019 (153)
56	EVA	ss3767803927	Jul 13, 2019 (153)
57	PACBIO	ss3786105361	Jul 13, 2019 (153)
58	PACBIO	ss3791369223	Jul 13, 2019 (153)
59	PACBIO	ss3796250486	Jul 13, 2019 (153)
60	KHV_HUMAN_GENOMES	ss3810965143	Jul 13, 2019 (153)
61	EVA	ss3831090244	Apr 26, 2020 (154)
62	EVA	ss3839055198	Apr 26, 2020 (154)
63	EVA	ss3844513550	Apr 26, 2020 (154)
64	SGDP_PRJ	ss3869579388	Apr 26, 2020 (154)
65	KRGDB	ss3917016320	Apr 26, 2020 (154)
66	KOGIC	ss3963540305	Apr 26, 2020 (154)
67	TOPMED	ss4780353237	Apr 26, 2021 (155)
68	TOMMO_GENOMICS	ss5187952767	Apr 26, 2021 (155)
69	1000G_HIGH_COVERAGE	ss5276565710	Oct 16, 2022 (156)
70	HUGCELL_USP	ss5473194807	Oct 16, 2022 (156)
71	EVA	ss5509298907	Oct 16, 2022 (156)
72	1000G_HIGH_COVERAGE	ss5566604802	Oct 16, 2022 (156)
73	SANFORD_IMAGENETICS	ss5645058910	Oct 16, 2022 (156)
74	TOMMO_GENOMICS	ss5729656765	Oct 16, 2022 (156)
75	YY_MCH	ss5809575059	Oct 16, 2022 (156)
76	EVA	ss5830316747	Oct 16, 2022 (156)
77	EVA	ss5856316734	Oct 16, 2022 (156)
78	EVA	ss5888296901	Oct 16, 2022 (156)
79	EVA	ss5974247000	Oct 16, 2022 (156)
80	EVA	ss5980497284	Oct 16, 2022 (156)
81	1000Genomes	NC_000008.10 - 28413948	Oct 12, 2018 (152)
82	1000Genomes_30x	NC_000008.11 - 28556431	Oct 16, 2022 (156)
83	The Avon Longitudinal Study of Parents and Children	NC_000008.10 - 28413948	Oct 12, 2018 (152)
84	Genetic variation in the Estonian population	NC_000008.10 - 28413948	Oct 12, 2018 (152)
85	The Danish reference pan genome	NC_000008.10 - 28413948	Apr 26, 2020 (154)
86	gnomAD - Genomes	NC_000008.11 - 28556431	Apr 26, 2021 (155)
87	Genome of the Netherlands Release 5	NC_000008.10 - 28413948	Apr 26, 2020 (154)
88	HapMap	NC_000008.11 - 28556431	Apr 26, 2020 (154)
89	KOREAN population from KRGDB	NC_000008.10 - 28413948	Apr 26, 2020 (154)
90	Korean Genome Project	NC_000008.11 - 28556431	Apr 26, 2020 (154)
91	Northern Sweden	NC_000008.10 - 28413948	Jul 13, 2019 (153)
92	Qatari	NC_000008.10 - 28413948	Apr 26, 2020 (154)
93	SGDP_PRJ	NC_000008.10 - 28413948	Apr 26, 2020 (154)
94	Siberian	NC_000008.10 - 28413948	Apr 26, 2020 (154)
95	8.3KJPN	NC_000008.10 - 28413948	Apr 26, 2021 (155)
96	14KJPN	NC_000008.11 - 28556431	Oct 16, 2022 (156)
97	TopMed	NC_000008.11 - 28556431	Apr 26, 2021 (155)
98	UK 10K study - Twins	NC_000008.10 - 28413948	Oct 12, 2018 (152)
99	A Vietnamese Genetic Variation Database	NC_000008.10 - 28413948	Jul 13, 2019 (153)
100	ALFA	NC_000008.11 - 28556431	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)
rs60292961	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
9897044152	NC_000008.11:28556430:T:A	NC_000008.11:28556430:T:A	(self)
ss77583182, ss80131256, ss85550217, ss93862493, ss112946606, ss115198023, ss115876921, ss164288650, ss166458330, ss198973475, ss206475824, ss254223814, ss279750899, ss285820169, ss294247828, ss1594937874	NC_000008.9:28469866:T:G	NC_000008.11:28556430:T:G	(self)
41288271, 22958330, 16335139, 8787720, 10257038, 24193714, 8812134, 10675931, 21596368, 5758284, 45922074, 22958330, 5119106, ss223624584, ss234380920, ss241249960, ss560647441, ss655081599, ss985344533, ss1075394182, ss1329184899, ss1431464237, ss1582622782, ss1620281417, ss1663275450, ss1805465749, ss1928634001, ss1970947126, ss2025019886, ss2153241930, ss2626993751, ss2709004438, ss2864842500, ss3002911718, ss3348112881, ss3670596891, ss3735527269, ss3767803927, ss3786105361, ss3791369223, ss3796250486, ss3831090244, ss3839055198, ss3869579388, ss3917016320, ss5187952767, ss5509298907, ss5645058910, ss5830316747, ss5974247000, ss5980497284	NC_000008.10:28413947:T:G	NC_000008.11:28556430:T:G	(self)
54130737, 291107622, 3595084, 19918306, 63493869, 617730797, 9897044152, ss2301849663, ss3026301287, ss3648883753, ss3721693764, ss3810965143, ss3844513550, ss3963540305, ss4780353237, ss5276565710, ss5473194807, ss5566604802, ss5729656765, ss5809575059, ss5856316734, ss5888296901	NC_000008.11:28556430:T:G	NC_000008.11:28556430:T:G	(self)
ss17236531, ss22692294	NT_023666.16:6788234:T:G	NC_000008.11:28556430:T:G	(self)
ss1323082, ss5490555, ss5693416, ss43255696, ss97862777, ss105609251, ss134437374, ss143364026, ss156198724	NT_167187.1:16272093:T:G	NC_000008.11:28556430:T:G	(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 rs893306

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

rs893306