Name: rs17054099
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.

rs17054099

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:156963969 (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 / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.037848 (10018/264690, TOPMED)
A=0.035933 (5034/140094, GnomAD)
A=0.05363 (4221/78702, PAGE_STUDY) (+ 17 more)
A=0.02263 (976/43122, ALFA)
A=0.02728 (771/28258, 14KJPN)
A=0.02786 (467/16760, 8.3KJPN)
A=0.0531 (340/6404, 1000G_30x)
A=0.0481 (241/5008, 1000G)
A=0.0096 (43/4480, Estonian)
A=0.0067 (26/3854, ALSPAC)
A=0.0049 (18/3708, TWINSUK)
A=0.0380 (111/2922, KOREAN)
A=0.0740 (100/1352, HapMap)
A=0.009 (9/998, GoNL)
A=0.005 (3/626, Chileans)
A=0.017 (10/600, NorthernSweden)
A=0.005 (1/216, Qatari)
A=0.093 (20/216, Vietnamese)
G=0.50 (8/16, SGDP_PRJ)
A=0.50 (8/16, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TIMD4 : 2KB Upstream 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	43122	G=0.97737	A=0.02263
European	Sub	30078	G=0.99302	A=0.00698
African	Sub	6760	G=0.8994	A=0.1006
African Others	Sub	222	G=0.892	A=0.108
African American	Sub	6538	G=0.8997	A=0.1003
Asian	Sub	524	G=0.966	A=0.034
East Asian	Sub	424	G=0.965	A=0.035
Other Asian	Sub	100	G=0.97	A=0.03
Latin American 1	Sub	588	G=0.978	A=0.022
Latin American 2	Sub	986	G=0.993	A=0.007
South Asian	Sub	180	G=1.000	A=0.000
Other	Sub	4006	G=0.9880	A=0.0120

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=0.962152	A=0.037848
gnomAD - Genomes	Global	Study-wide	140094	G=0.964067	A=0.035933
gnomAD - Genomes	European	Sub	75886	G=0.99262	A=0.00738
gnomAD - Genomes	African	Sub	41960	G=0.90217	A=0.09783
gnomAD - Genomes	American	Sub	13650	G=0.98974	A=0.01026
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.9961	A=0.0039
gnomAD - Genomes	East Asian	Sub	3132	G=0.9483	A=0.0517
gnomAD - Genomes	Other	Sub	2148	G=0.9749	A=0.0251
The PAGE Study	Global	Study-wide	78702	G=0.94637	A=0.05363
The PAGE Study	AfricanAmerican	Sub	32516	G=0.90171	A=0.09829
The PAGE Study	Mexican	Sub	10810	G=0.99232	A=0.00768
The PAGE Study	Asian	Sub	8318	G=0.9666	A=0.0334
The PAGE Study	PuertoRican	Sub	7918	G=0.9717	A=0.0283
The PAGE Study	NativeHawaiian	Sub	4534	G=0.9810	A=0.0190
The PAGE Study	Cuban	Sub	4230	G=0.9811	A=0.0189
The PAGE Study	Dominican	Sub	3828	G=0.9506	A=0.0494
The PAGE Study	CentralAmerican	Sub	2450	G=0.9812	A=0.0188
The PAGE Study	SouthAmerican	Sub	1982	G=0.9909	A=0.0091
The PAGE Study	NativeAmerican	Sub	1260	G=0.9857	A=0.0143
The PAGE Study	SouthAsian	Sub	856	G=0.996	A=0.004
Allele Frequency Aggregator	Total	Global	43122	G=0.97737	A=0.02263
Allele Frequency Aggregator	European	Sub	30078	G=0.99302	A=0.00698
Allele Frequency Aggregator	African	Sub	6760	G=0.8994	A=0.1006
Allele Frequency Aggregator	Other	Sub	4006	G=0.9880	A=0.0120
Allele Frequency Aggregator	Latin American 2	Sub	986	G=0.993	A=0.007
Allele Frequency Aggregator	Latin American 1	Sub	588	G=0.978	A=0.022
Allele Frequency Aggregator	Asian	Sub	524	G=0.966	A=0.034
Allele Frequency Aggregator	South Asian	Sub	180	G=1.000	A=0.000
14KJPN	JAPANESE	Study-wide	28258	G=0.97272	A=0.02728
8.3KJPN	JAPANESE	Study-wide	16760	G=0.97214	A=0.02786
1000Genomes_30x	Global	Study-wide	6404	G=0.9469	A=0.0531
1000Genomes_30x	African	Sub	1786	G=0.8651	A=0.1349
1000Genomes_30x	Europe	Sub	1266	G=0.9953	A=0.0047
1000Genomes_30x	South Asian	Sub	1202	G=0.9983	A=0.0017
1000Genomes_30x	East Asian	Sub	1170	G=0.9308	A=0.0692
1000Genomes_30x	American	Sub	980	G=0.990	A=0.010
1000Genomes	Global	Study-wide	5008	G=0.9519	A=0.0481
1000Genomes	African	Sub	1322	G=0.8707	A=0.1293
1000Genomes	East Asian	Sub	1008	G=0.9415	A=0.0585
1000Genomes	Europe	Sub	1006	G=0.9960	A=0.0040
1000Genomes	South Asian	Sub	978	G=0.999	A=0.001
1000Genomes	American	Sub	694	G=0.991	A=0.009
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.9904	A=0.0096
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9933	A=0.0067
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9951	A=0.0049
KOREAN population from KRGDB	KOREAN	Study-wide	2922	G=0.9620	A=0.0380
HapMap	Global	Study-wide	1352	G=0.9260	A=0.0740
HapMap	African	Sub	692	G=0.900	A=0.100
HapMap	American	Sub	488	G=0.945	A=0.055
HapMap	Asian	Sub	172	G=0.977	A=0.023
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.991	A=0.009
Chileans	Chilean	Study-wide	626	G=0.995	A=0.005
Northern Sweden	ACPOP	Study-wide	600	G=0.983	A=0.017
Qatari	Global	Study-wide	216	G=0.995	A=0.005
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.907	A=0.093
SGDP_PRJ	Global	Study-wide	16	G=0.50	A=0.50

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 5	NC_000005.10:g.156963969G>A
GRCh38.p14 chr 5	NC_000005.10:g.156963969G>C
GRCh38.p14 chr 5	NC_000005.10:g.156963969G>T
GRCh37.p13 chr 5	NC_000005.9:g.156390980G>A
GRCh37.p13 chr 5	NC_000005.9:g.156390980G>C
GRCh37.p13 chr 5	NC_000005.9:g.156390980G>T

Gene: TIMD4, T cell immunoglobulin and mucin domain containing 4 (minus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
TIMD4 transcript variant 2	NM_001146726.2:c.	N/A	Upstream Transcript Variant
TIMD4 transcript variant 1	NM_138379.3:c.	N/A	Upstream Transcript Variant
TIMD4 transcript variant X2	XM_011534694.3:c.	N/A	Upstream Transcript Variant
TIMD4 transcript variant X1	XM_017010021.2:c.	N/A	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	G=	A	C	T
GRCh38.p14 chr 5	NC_000005.10:g.156963969=	NC_000005.10:g.156963969G>A	NC_000005.10:g.156963969G>C	NC_000005.10:g.156963969G>T
GRCh37.p13 chr 5	NC_000005.9:g.156390980=	NC_000005.9:g.156390980G>A	NC_000005.9:g.156390980G>C	NC_000005.9:g.156390980G>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#.

57 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	PERLEGEN	ss23472346	Sep 20, 2004 (123)
2	AFFY	ss66274545	Jul 04, 2010 (132)
3	ILLUMINA	ss75082007	Dec 07, 2007 (129)
4	AFFY	ss75924912	Dec 08, 2007 (130)
5	KRIBB_YJKIM	ss83169328	Dec 15, 2007 (130)
6	1000GENOMES	ss113515132	Jan 25, 2009 (130)
7	ILLUMINA	ss160416710	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss166016738	Jul 04, 2010 (132)
9	AFFY	ss169199226	Jul 04, 2010 (132)
10	ILLUMINA	ss172724399	Jul 04, 2010 (132)
11	1000GENOMES	ss222061203	Jul 14, 2010 (132)
12	ILLUMINA	ss480883261	Sep 08, 2015 (146)
13	ILLUMINA	ss536939518	Sep 08, 2015 (146)
14	TISHKOFF	ss558823930	Apr 25, 2013 (138)
15	SSMP	ss652729068	Apr 25, 2013 (138)
16	EVA-GONL	ss982303975	Aug 21, 2014 (142)
17	JMKIDD_LAB	ss1073175987	Aug 21, 2014 (142)
18	1000GENOMES	ss1317922437	Aug 21, 2014 (142)
19	EVA_DECODE	ss1591841482	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1614393582	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1657387615	Apr 01, 2015 (144)
22	EVA_SVP	ss1712813966	Apr 01, 2015 (144)
23	WEILL_CORNELL_DGM	ss1925558468	Feb 12, 2016 (147)
24	ILLUMINA	ss1958838328	Feb 12, 2016 (147)
25	HUMAN_LONGEVITY	ss2279633913	Dec 20, 2016 (150)
26	GRF	ss2707120252	Nov 08, 2017 (151)
27	GNOMAD	ss2832794781	Nov 08, 2017 (151)
28	SWEGEN	ss2998075607	Nov 08, 2017 (151)
29	ILLUMINA	ss3022547077	Nov 08, 2017 (151)
30	ILLUMINA	ss3629381460	Oct 12, 2018 (152)
31	ILLUMINA	ss3636744268	Oct 12, 2018 (152)
32	ILLUMINA	ss3638591210	Oct 12, 2018 (152)
33	ILLUMINA	ss3643534319	Oct 12, 2018 (152)
34	ILLUMINA	ss3653051708	Oct 12, 2018 (152)
35	EGCUT_WGS	ss3665999542	Jul 13, 2019 (153)
36	EVA_DECODE	ss3716045853	Jul 13, 2019 (153)
37	ILLUMINA	ss3726286278	Jul 13, 2019 (153)
38	ACPOP	ss3732966189	Jul 13, 2019 (153)
39	EVA	ss3764281325	Jul 13, 2019 (153)
40	PAGE_CC	ss3771243453	Jul 13, 2019 (153)
41	KHV_HUMAN_GENOMES	ss3807447851	Jul 13, 2019 (153)
42	SGDP_PRJ	ss3863341340	Apr 26, 2020 (154)
43	KRGDB	ss3910028473	Apr 26, 2020 (154)
44	EVA	ss4017240759	Apr 26, 2021 (155)
45	TOPMED	ss4684873701	Apr 26, 2021 (155)
46	TOMMO_GENOMICS	ss5174940732	Apr 26, 2021 (155)
47	1000G_HIGH_COVERAGE	ss5266459672	Oct 13, 2022 (156)
48	EVA	ss5362100591	Oct 13, 2022 (156)
49	HUGCELL_USP	ss5464361187	Oct 13, 2022 (156)
50	1000G_HIGH_COVERAGE	ss5551425361	Oct 13, 2022 (156)
51	SANFORD_IMAGENETICS	ss5639230887	Oct 13, 2022 (156)
52	TOMMO_GENOMICS	ss5712249623	Oct 13, 2022 (156)
53	YY_MCH	ss5806916559	Oct 13, 2022 (156)
54	EVA	ss5835882112	Oct 13, 2022 (156)
55	EVA	ss5855088759	Oct 13, 2022 (156)
56	EVA	ss5897039730	Oct 13, 2022 (156)
57	EVA	ss5967717414	Oct 13, 2022 (156)
58	1000Genomes	NC_000005.9 - 156390980	Oct 12, 2018 (152)
59	1000Genomes_30x	NC_000005.10 - 156963969	Oct 13, 2022 (156)
60	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 156390980	Oct 12, 2018 (152)
61	Chileans	NC_000005.9 - 156390980	Apr 26, 2020 (154)
62	Genetic variation in the Estonian population	NC_000005.9 - 156390980	Oct 12, 2018 (152)
63	gnomAD - Genomes	NC_000005.10 - 156963969	Apr 26, 2021 (155)
64	Genome of the Netherlands Release 5	NC_000005.9 - 156390980	Apr 26, 2020 (154)
65	HapMap	NC_000005.10 - 156963969	Apr 26, 2020 (154)
66	KOREAN population from KRGDB	NC_000005.9 - 156390980	Apr 26, 2020 (154)
67	Northern Sweden	NC_000005.9 - 156390980	Jul 13, 2019 (153)
68	The PAGE Study	NC_000005.10 - 156963969	Jul 13, 2019 (153)
69	Qatari	NC_000005.9 - 156390980	Apr 26, 2020 (154)
70	SGDP_PRJ	NC_000005.9 - 156390980	Apr 26, 2020 (154)
71	8.3KJPN	NC_000005.9 - 156390980	Apr 26, 2021 (155)
72	14KJPN	NC_000005.10 - 156963969	Oct 13, 2022 (156)
73	TopMed	NC_000005.10 - 156963969	Apr 26, 2021 (155)
74	UK 10K study - Twins	NC_000005.9 - 156390980	Oct 12, 2018 (152)
75	A Vietnamese Genetic Variation Database	NC_000005.9 - 156390980	Jul 13, 2019 (153)
76	ALFA	NC_000005.10 - 156963969	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)
rs56464852	May 23, 2008 (130)
rs58768538	Feb 25, 2009 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss113515132, ss166016738, ss1591841482, ss1712813966, ss3643534319	NC_000005.8:156323557:G:A	NC_000005.10:156963968:G:A	(self)
29625755, 16488714, 363452, 11737790, 7318502, 17205867, 6251054, 7600398, 15358320, 32910039, 16488714, 3654306, ss222061203, ss480883261, ss536939518, ss558823930, ss652729068, ss982303975, ss1073175987, ss1317922437, ss1614393582, ss1657387615, ss1925558468, ss1958838328, ss2707120252, ss2832794781, ss2998075607, ss3022547077, ss3629381460, ss3636744268, ss3638591210, ss3653051708, ss3665999542, ss3732966189, ss3764281325, ss3863341340, ss3910028473, ss4017240759, ss5174940732, ss5362100591, ss5639230887, ss5835882112, ss5967717414	NC_000005.9:156390979:G:A	NC_000005.10:156963968:G:A	(self)
38951296, 209533928, 3005180, 464922, 46086727, 522251258, 10152306840, ss2279633913, ss3716045853, ss3726286278, ss3771243453, ss3807447851, ss4684873701, ss5266459672, ss5464361187, ss5551425361, ss5712249623, ss5806916559, ss5855088759, ss5897039730	NC_000005.10:156963968:G:A	NC_000005.10:156963968:G:A	(self)
ss23472346, ss75082007, ss75924912, ss83169328, ss160416710, ss169199226, ss172724399	NT_023133.13:1202252:G:A	NC_000005.10:156963968:G:A	(self)
ss66274545	NT_023133.14:1202644:G:C	NC_000005.10:156963968:G:C	(self)
ss66274545	NT_023133.14:1202644:G:T	NC_000005.10:156963968:G: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 rs17054099

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

rs17054099