Name: rs11704416
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.

rs11704416

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr22:40040969 (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: G>A / G>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.199475 (52799/264690, TOPMED)
C=0.03118 (881/28258, 14KJPN)
C=0.19995 (3777/18890, ALFA) (+ 18 more)
C=0.03043 (510/16760, 8.3KJPN)
C=0.2010 (1287/6404, 1000G_30x)
C=0.2013 (1008/5008, 1000G)
C=0.2016 (903/4480, Estonian)
C=0.2039 (786/3854, ALSPAC)
C=0.2025 (751/3708, TWINSUK)
C=0.0438 (128/2922, KOREAN)
C=0.0338 (62/1832, Korea1K)
C=0.185 (185/998, GoNL)
C=0.026 (20/776, PRJEB37584)
C=0.165 (99/600, NorthernSweden)
C=0.198 (64/324, HapMap)
C=0.176 (38/216, Qatari)
C=0.042 (9/216, Vietnamese)
G=0.456 (73/160, SGDP_PRJ)
C=0.21 (14/66, Ancient Sardinia)
C=0.17 (7/40, GENOME_DK)
G=0.44 (7/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FAM83F : 3 Prime UTR Variant
Publications: 3 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	18890	G=0.80005	C=0.19995
European	Sub	14286	G=0.80456	C=0.19544
African	Sub	2946	G=0.7447	C=0.2553
African Others	Sub	114	G=0.772	C=0.228
African American	Sub	2832	G=0.7436	C=0.2564
Asian	Sub	112	G=0.991	C=0.009
East Asian	Sub	86	G=1.00	C=0.00
Other Asian	Sub	26	G=0.96	C=0.04
Latin American 1	Sub	146	G=0.822	C=0.178
Latin American 2	Sub	610	G=0.907	C=0.093
South Asian	Sub	98	G=0.77	C=0.23
Other	Sub	692	G=0.818	C=0.182

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	G=0.800525	C=0.199475
14KJPN	JAPANESE	Study-wide	28258	G=0.96882	C=0.03118
Allele Frequency Aggregator	Total	Global	18890	G=0.80005	C=0.19995
Allele Frequency Aggregator	European	Sub	14286	G=0.80456	C=0.19544
Allele Frequency Aggregator	African	Sub	2946	G=0.7447	C=0.2553
Allele Frequency Aggregator	Other	Sub	692	G=0.818	C=0.182
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.907	C=0.093
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.822	C=0.178
Allele Frequency Aggregator	Asian	Sub	112	G=0.991	C=0.009
Allele Frequency Aggregator	South Asian	Sub	98	G=0.77	C=0.23
8.3KJPN	JAPANESE	Study-wide	16760	G=0.96957	C=0.03043
1000Genomes_30x	Global	Study-wide	6404	G=0.7990	C=0.2010
1000Genomes_30x	African	Sub	1786	G=0.7032	C=0.2968
1000Genomes_30x	Europe	Sub	1266	G=0.8081	C=0.1919
1000Genomes_30x	South Asian	Sub	1202	G=0.6880	C=0.3120
1000Genomes_30x	East Asian	Sub	1170	G=0.9769	C=0.0231
1000Genomes_30x	American	Sub	980	G=0.886	C=0.114
1000Genomes	Global	Study-wide	5008	G=0.7987	C=0.2013
1000Genomes	African	Sub	1322	G=0.6944	C=0.3056
1000Genomes	East Asian	Sub	1008	G=0.9782	C=0.0218
1000Genomes	Europe	Sub	1006	G=0.8012	C=0.1988
1000Genomes	South Asian	Sub	978	G=0.689	C=0.311
1000Genomes	American	Sub	694	G=0.888	C=0.112
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7984	C=0.2016
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.7961	C=0.2039
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.7975	C=0.2025
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9562	C=0.0438
Korean Genome Project	KOREAN	Study-wide	1832	G=0.9662	C=0.0338
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.815	C=0.185
CNV burdens in cranial meningiomas	Global	Study-wide	776	G=0.974	C=0.026
CNV burdens in cranial meningiomas	CRM	Sub	776	G=0.974	C=0.026
Northern Sweden	ACPOP	Study-wide	600	G=0.835	C=0.165
HapMap	Global	Study-wide	324	G=0.802	C=0.198
HapMap	African	Sub	120	G=0.675	C=0.325
HapMap	American	Sub	118	G=0.805	C=0.195
HapMap	Asian	Sub	86	G=0.98	C=0.02
Qatari	Global	Study-wide	216	G=0.824	C=0.176
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.958	C=0.042
SGDP_PRJ	Global	Study-wide	160	G=0.456	C=0.544
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	66	G=0.79	C=0.21
The Danish reference pan genome	Danish	Study-wide	40	G=0.82	C=0.17
Siberian	Global	Study-wide	16	G=0.44	C=0.56

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 22	NC_000022.11:g.40040969G>A
GRCh38.p14 chr 22	NC_000022.11:g.40040969G>C
GRCh37.p13 chr 22	NC_000022.10:g.40436973G>A
GRCh37.p13 chr 22	NC_000022.10:g.40436973G>C

Gene: FAM83F, family with sequence similarity 83 member F (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FAM83F transcript	NM_138435.4:c.*11404=	N/A	3 Prime UTR 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	G=	A	C
GRCh38.p14 chr 22	NC_000022.11:g.40040969=	NC_000022.11:g.40040969G>A	NC_000022.11:g.40040969G>C
GRCh37.p13 chr 22	NC_000022.10:g.40436973=	NC_000022.10:g.40436973G>A	NC_000022.10:g.40436973G>C
FAM83F transcript	NM_138435.4:c.*11404=	NM_138435.4:c.*11404G>A	NM_138435.4:c.*11404G>C
FAM83F transcript	NM_138435.3:c.*11404=	NM_138435.3:c.*11404G>A	NM_138435.3:c.*11404G>C

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#.

72 SubSNP, 23 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	CSHL-HAPMAP	ss16926877	Feb 28, 2004 (120)
2	ABI	ss44329205	Mar 13, 2006 (126)
3	SI_EXO	ss52069429	Oct 16, 2006 (127)
4	ILLUMINA-UK	ss117413100	Feb 14, 2009 (130)
5	BUSHMAN	ss204096447	Jul 04, 2010 (132)
6	BCM-HGSC-SUB	ss208844189	Jul 04, 2010 (132)
7	1000GENOMES	ss212123892	Jul 14, 2010 (132)
8	1000GENOMES	ss228693299	Jul 14, 2010 (132)
9	1000GENOMES	ss238078436	Jul 15, 2010 (132)
10	1000GENOMES	ss244194500	Jul 15, 2010 (132)
11	GMI	ss283644963	May 04, 2012 (137)
12	ILLUMINA	ss483952200	May 04, 2012 (137)
13	ILLUMINA	ss484316380	May 04, 2012 (137)
14	ILLUMINA	ss536146144	Sep 08, 2015 (146)
15	TISHKOFF	ss566659253	Apr 25, 2013 (138)
16	SSMP	ss662588393	Apr 25, 2013 (138)
17	ILLUMINA	ss779154965	Sep 08, 2015 (146)
18	ILLUMINA	ss782420038	Sep 08, 2015 (146)
19	ILLUMINA	ss834619908	Sep 08, 2015 (146)
20	EVA-GONL	ss995380191	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1082678870	Aug 21, 2014 (142)
22	1000GENOMES	ss1367281155	Aug 21, 2014 (142)
23	DDI	ss1429264782	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1579763142	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1640054215	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1683048248	Apr 01, 2015 (144)
27	EVA_DECODE	ss1699451585	Apr 01, 2015 (144)
28	HAMMER_LAB	ss1809801583	Sep 08, 2015 (146)
29	WEILL_CORNELL_DGM	ss1938948311	Feb 12, 2016 (147)
30	JJLAB	ss2030246515	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2158866189	Dec 20, 2016 (150)
32	HUMAN_LONGEVITY	ss2247564909	Dec 20, 2016 (150)
33	ILLUMINA	ss2633882359	Nov 08, 2017 (151)
34	GRF	ss2704618980	Nov 08, 2017 (151)
35	GNOMAD	ss2974717267	Nov 08, 2017 (151)
36	AFFY	ss2985857270	Nov 08, 2017 (151)
37	SWEGEN	ss3019351272	Nov 08, 2017 (151)
38	ILLUMINA	ss3022189664	Nov 08, 2017 (151)
39	BIOINF_KMB_FNS_UNIBA	ss3028959872	Nov 08, 2017 (151)
40	CSHL	ss3352850489	Nov 08, 2017 (151)
41	ILLUMINA	ss3628541704	Oct 12, 2018 (152)
42	ILLUMINA	ss3631833299	Oct 12, 2018 (152)
43	ILLUMINA	ss3652653885	Oct 12, 2018 (152)
44	EGCUT_WGS	ss3685845036	Jul 13, 2019 (153)
45	EVA_DECODE	ss3708259441	Jul 13, 2019 (153)
46	ILLUMINA	ss3725971538	Jul 13, 2019 (153)
47	ACPOP	ss3743958444	Jul 13, 2019 (153)
48	EVA	ss3759418806	Jul 13, 2019 (153)
49	KHV_HUMAN_GENOMES	ss3822579846	Jul 13, 2019 (153)
50	EVA	ss3836006199	Apr 27, 2020 (154)
51	EVA	ss3841631786	Apr 27, 2020 (154)
52	EVA	ss3847146937	Apr 27, 2020 (154)
53	SGDP_PRJ	ss3890609470	Apr 27, 2020 (154)
54	KRGDB	ss3940996654	Apr 27, 2020 (154)
55	KOGIC	ss3983702126	Apr 27, 2020 (154)
56	EVA	ss3984761020	Apr 26, 2021 (155)
57	EVA	ss3985919709	Apr 26, 2021 (155)
58	TOPMED	ss5110234325	Apr 26, 2021 (155)
59	TOMMO_GENOMICS	ss5232763511	Apr 26, 2021 (155)
60	1000G_HIGH_COVERAGE	ss5311205072	Oct 16, 2022 (156)
61	EVA	ss5441494449	Oct 16, 2022 (156)
62	HUGCELL_USP	ss5503036665	Oct 16, 2022 (156)
63	EVA	ss5512387980	Oct 16, 2022 (156)
64	1000G_HIGH_COVERAGE	ss5618809548	Oct 16, 2022 (156)
65	SANFORD_IMAGENETICS	ss5624503995	Oct 16, 2022 (156)
66	SANFORD_IMAGENETICS	ss5664550776	Oct 16, 2022 (156)
67	TOMMO_GENOMICS	ss5793929464	Oct 16, 2022 (156)
68	YY_MCH	ss5818737205	Oct 16, 2022 (156)
69	EVA	ss5822112701	Oct 16, 2022 (156)
70	EVA	ss5853405215	Oct 16, 2022 (156)
71	EVA	ss5881939539	Oct 16, 2022 (156)
72	EVA	ss5959408042	Oct 16, 2022 (156)
73	1000Genomes	NC_000022.10 - 40436973	Oct 12, 2018 (152)
74	1000Genomes_30x	NC_000022.11 - 40040969	Oct 16, 2022 (156)
75	The Avon Longitudinal Study of Parents and Children	NC_000022.10 - 40436973	Oct 12, 2018 (152)
76	Genetic variation in the Estonian population	NC_000022.10 - 40436973	Oct 12, 2018 (152)
77	The Danish reference pan genome	NC_000022.10 - 40436973	Apr 27, 2020 (154)
78	gnomAD - Genomes Submission ignored due to conflicting rows: Row 570813609 (NC_000022.11:40040968:G:A 1/140144) Row 570813610 (NC_000022.11:40040968:G:C 28771/140122)	-	Apr 26, 2021 (155)
79	gnomAD - Genomes Submission ignored due to conflicting rows: Row 570813609 (NC_000022.11:40040968:G:A 1/140144) Row 570813610 (NC_000022.11:40040968:G:C 28771/140122)	-	Apr 26, 2021 (155)
80	Genome of the Netherlands Release 5	NC_000022.10 - 40436973	Apr 27, 2020 (154)
81	HapMap	NC_000022.11 - 40040969	Apr 27, 2020 (154)
82	KOREAN population from KRGDB	NC_000022.10 - 40436973	Apr 27, 2020 (154)
83	Korean Genome Project	NC_000022.11 - 40040969	Apr 27, 2020 (154)
84	Northern Sweden	NC_000022.10 - 40436973	Jul 13, 2019 (153)
85	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000022.10 - 40436973	Apr 26, 2021 (155)
86	CNV burdens in cranial meningiomas	NC_000022.10 - 40436973	Apr 26, 2021 (155)
87	Qatari	NC_000022.10 - 40436973	Apr 27, 2020 (154)
88	SGDP_PRJ	NC_000022.10 - 40436973	Apr 27, 2020 (154)
89	Siberian	NC_000022.10 - 40436973	Apr 27, 2020 (154)
90	8.3KJPN	NC_000022.10 - 40436973	Apr 26, 2021 (155)
91	14KJPN	NC_000022.11 - 40040969	Oct 16, 2022 (156)
92	TopMed	NC_000022.11 - 40040969	Apr 26, 2021 (155)
93	UK 10K study - Twins	NC_000022.10 - 40436973	Oct 12, 2018 (152)
94	A Vietnamese Genetic Variation Database	NC_000022.10 - 40436973	Jul 13, 2019 (153)
95	ALFA	NC_000022.11 - 40040969	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
	NC_000022.11:40040968:G:A	NC_000022.11:40040968:G:A	(self)
ss117413100, ss204096447, ss208844189, ss212123892, ss283644963, ss484316380, ss1699451585	NC_000022.9:38766918:G:C	NC_000022.11:40040968:G:C	(self)
80837396, 44714735, 31583284, 5928081, 19923077, 48174048, 17243309, 1145636, 310606, 20990233, 42626450, 11382543, 90732818, 44714735, 9863274, ss228693299, ss238078436, ss244194500, ss483952200, ss536146144, ss566659253, ss662588393, ss779154965, ss782420038, ss834619908, ss995380191, ss1082678870, ss1367281155, ss1429264782, ss1579763142, ss1640054215, ss1683048248, ss1809801583, ss1938948311, ss2030246515, ss2158866189, ss2633882359, ss2704618980, ss2974717267, ss2985857270, ss3019351272, ss3022189664, ss3352850489, ss3628541704, ss3631833299, ss3652653885, ss3685845036, ss3743958444, ss3759418806, ss3836006199, ss3841631786, ss3890609470, ss3940996654, ss3984761020, ss3985919709, ss5232763511, ss5441494449, ss5512387980, ss5624503995, ss5664550776, ss5822112701, ss5959408042	NC_000022.10:40436972:G:C	NC_000022.11:40040968:G:C	(self)
106335483, 2261143, 40080127, 127766568, 385343272, 953183202, ss2247564909, ss3028959872, ss3708259441, ss3725971538, ss3822579846, ss3847146937, ss3983702126, ss5110234325, ss5311205072, ss5503036665, ss5618809548, ss5793929464, ss5818737205, ss5853405215, ss5881939539	NC_000022.11:40040968:G:C	NC_000022.11:40040968:G:C	(self)
ss16926877	NT_011520.9:19746026:G:C	NC_000022.11:40040968:G:C	(self)
ss52069429	NT_011520.10:19827487:G:C	NC_000022.11:40040968:G:C	(self)
ss44329205	NT_011520.12:19827541:G:C	NC_000022.11:40040968:G:C	(self)

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

3 citations for rs11704416

PMID	Title	Author	Year	Journal
28399564	Interactions Between Genome-Wide Significant Genetic Variants and Circulating Concentrations of 25-Hydroxyvitamin D in Relation to Prostate Cancer Risk in the National Cancer Institute BPC3.	Dimitrakopoulou VI et al.	2017	American journal of epidemiology
29101112	Prostate Cancer Germline Variations and Implications for Screening and Treatment.	Dias A et al.	2018	Cold Spring Harbor perspectives in medicine
32341752	Association of germline genetic variants with TMPRSS2-ERG fusion status in prostate cancer.	Kohaar I et al.	2020	Oncotarget

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

rs11704416