Name: rs25855
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.

rs25855

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr5:157197389 (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: A>C / A>G
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.156217 (41349/264690, TOPMED)
A=0.155018 (21727/140158, GnomAD)
A=0.36818 (10404/28258, 14KJPN) (+ 17 more)
A=0.17829 (4375/24538, ALFA)
A=0.36599 (6134/16760, 8.3KJPN)
A=0.1744 (1117/6404, 1000G_30x)
A=0.1785 (894/5008, 1000G)
A=0.2016 (903/4480, Estonian)
A=0.1850 (713/3854, ALSPAC)
A=0.2023 (750/3708, TWINSUK)
A=0.4010 (1175/2930, KOREAN)
A=0.3745 (686/1832, Korea1K)
A=0.1771 (284/1604, HapMap)
A=0.203 (203/998, GoNL)
A=0.210 (126/600, NorthernSweden)
A=0.180 (92/510, SGDP_PRJ)
A=0.093 (20/216, Qatari)
A=0.271 (58/214, Vietnamese)
A=0.17 (9/52, Siberian)
A=0.15 (6/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ITK : Intron Variant
Publications: 2 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	24538	A=0.17829	C=0.00000, G=0.82171
European	Sub	16762	A=0.19628	C=0.00000, G=0.80372
African	Sub	3102	A=0.0355	C=0.0000, G=0.9645
African Others	Sub	102	A=0.000	C=0.000, G=1.000
African American	Sub	3000	A=0.0367	C=0.0000, G=0.9633
Asian	Sub	160	A=0.306	C=0.000, G=0.694
East Asian	Sub	102	A=0.324	C=0.000, G=0.676
Other Asian	Sub	58	A=0.28	C=0.00, G=0.72
Latin American 1	Sub	292	A=0.175	C=0.000, G=0.825
Latin American 2	Sub	2770	A=0.2217	C=0.0000, G=0.7783
South Asian	Sub	110	A=0.155	C=0.000, G=0.845
Other	Sub	1342	A=0.1818	C=0.0000, G=0.8182

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	A=0.156217	G=0.843783
gnomAD - Genomes	Global	Study-wide	140158	A=0.155018	G=0.844982
gnomAD - Genomes	European	Sub	75884	A=0.19747	G=0.80253
gnomAD - Genomes	African	Sub	42032	A=0.03921	G=0.96079
gnomAD - Genomes	American	Sub	13646	A=0.21567	G=0.78433
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	A=0.2530	G=0.7470
gnomAD - Genomes	East Asian	Sub	3124	A=0.3182	G=0.6818
gnomAD - Genomes	Other	Sub	2148	A=0.1471	G=0.8529
14KJPN	JAPANESE	Study-wide	28258	A=0.36818	G=0.63182
Allele Frequency Aggregator	Total	Global	24538	A=0.17829	C=0.00000, G=0.82171
Allele Frequency Aggregator	European	Sub	16762	A=0.19628	C=0.00000, G=0.80372
Allele Frequency Aggregator	African	Sub	3102	A=0.0355	C=0.0000, G=0.9645
Allele Frequency Aggregator	Latin American 2	Sub	2770	A=0.2217	C=0.0000, G=0.7783
Allele Frequency Aggregator	Other	Sub	1342	A=0.1818	C=0.0000, G=0.8182
Allele Frequency Aggregator	Latin American 1	Sub	292	A=0.175	C=0.000, G=0.825
Allele Frequency Aggregator	Asian	Sub	160	A=0.306	C=0.000, G=0.694
Allele Frequency Aggregator	South Asian	Sub	110	A=0.155	C=0.000, G=0.845
8.3KJPN	JAPANESE	Study-wide	16760	A=0.36599	G=0.63401
1000Genomes_30x	Global	Study-wide	6404	A=0.1744	G=0.8256
1000Genomes_30x	African	Sub	1786	A=0.0062	G=0.9938
1000Genomes_30x	Europe	Sub	1266	A=0.1864	G=0.8136
1000Genomes_30x	South Asian	Sub	1202	A=0.2072	G=0.7928
1000Genomes_30x	East Asian	Sub	1170	A=0.3316	G=0.6684
1000Genomes_30x	American	Sub	980	A=0.238	G=0.762
1000Genomes	Global	Study-wide	5008	A=0.1785	G=0.8215
1000Genomes	African	Sub	1322	A=0.0068	G=0.9932
1000Genomes	East Asian	Sub	1008	A=0.3244	G=0.6756
1000Genomes	Europe	Sub	1006	A=0.1769	G=0.8231
1000Genomes	South Asian	Sub	978	A=0.213	G=0.787
1000Genomes	American	Sub	694	A=0.248	G=0.752
Genetic variation in the Estonian population	Estonian	Study-wide	4480	A=0.2016	G=0.7984
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	A=0.1850	G=0.8150
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	A=0.2023	G=0.7977
KOREAN population from KRGDB	KOREAN	Study-wide	2930	A=0.4010	G=0.5990
Korean Genome Project	KOREAN	Study-wide	1832	A=0.3745	G=0.6255
HapMap	Global	Study-wide	1604	A=0.1771	G=0.8229
HapMap	American	Sub	770	A=0.214	G=0.786
HapMap	African	Sub	404	A=0.007	G=0.993
HapMap	Asian	Sub	254	A=0.350	G=0.650
HapMap	Europe	Sub	176	A=0.153	G=0.847
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	A=0.203	G=0.797
Northern Sweden	ACPOP	Study-wide	600	A=0.210	G=0.790
SGDP_PRJ	Global	Study-wide	510	A=0.180	G=0.820
Qatari	Global	Study-wide	216	A=0.093	G=0.907
A Vietnamese Genetic Variation Database	Global	Study-wide	214	A=0.271	G=0.729
Siberian	Global	Study-wide	52	A=0.17	G=0.83
The Danish reference pan genome	Danish	Study-wide	40	A=0.15	G=0.85

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.157197389A>C
GRCh38.p14 chr 5	NC_000005.10:g.157197389A>G
GRCh37.p13 chr 5	NC_000005.9:g.156624400A>C
GRCh37.p13 chr 5	NC_000005.9:g.156624400A>G
ITK RefSeqGene (LRG_189)	NG_016276.1:g.21494A>C
ITK RefSeqGene (LRG_189)	NG_016276.1:g.21494A>G

Gene: ITK, IL2 inducible T cell kinase (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ITK transcript	NM_005546.4:c.139-11500A>C	N/A	Intron 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	A=	C	G
GRCh38.p14 chr 5	NC_000005.10:g.157197389=	NC_000005.10:g.157197389A>C	NC_000005.10:g.157197389A>G
GRCh37.p13 chr 5	NC_000005.9:g.156624400=	NC_000005.9:g.156624400A>C	NC_000005.9:g.156624400A>G
ITK RefSeqGene (LRG_189)	NG_016276.1:g.21494=	NG_016276.1:g.21494A>C	NG_016276.1:g.21494A>G
ITK transcript	NM_005546.3:c.139-11500=	NM_005546.3:c.139-11500A>C	NM_005546.3:c.139-11500A>G
ITK transcript	NM_005546.4:c.139-11500=	NM_005546.4:c.139-11500A>C	NM_005546.4:c.139-11500A>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#.

93 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss29973	May 08, 2000 (76)
2	KWOK	ss31693	May 08, 2000 (76)
3	SC_JCM	ss486580	Jul 16, 2000 (80)
4	KWOK	ss1088398	Oct 04, 2000 (86)
5	KWOK	ss1088790	Oct 04, 2000 (86)
6	KWOK	ss1784560	Oct 18, 2000 (87)
7	KWOK	ss1784726	Oct 18, 2000 (87)
8	KWOK	ss1830774	Oct 18, 2000 (87)
9	TSC-CSHL	ss5177290	Oct 08, 2002 (108)
10	TSC-CSHL	ss5286468	Oct 08, 2002 (108)
11	SC_JCM	ss5885505	Feb 20, 2003 (111)
12	WI_SSAHASNP	ss6481691	Feb 20, 2003 (111)
13	WI_SSAHASNP	ss11731749	Jul 11, 2003 (116)
14	SC_SNP	ss14814072	Dec 05, 2003 (119)
15	CSHL-HAPMAP	ss17858617	Feb 27, 2004 (120)
16	SSAHASNP	ss22291603	Apr 05, 2004 (121)
17	AFFY	ss66253132	Dec 02, 2006 (127)
18	AFFY	ss76398509	Dec 08, 2007 (130)
19	HGSV	ss77280470	Dec 06, 2007 (129)
20	HGSV	ss81302801	Dec 15, 2007 (130)
21	KRIBB_YJKIM	ss81404749	Dec 15, 2007 (130)
22	HUMANGENOME_JCVI	ss98659375	Feb 05, 2009 (130)
23	BGI	ss104254886	Dec 01, 2009 (131)
24	1000GENOMES	ss109546564	Jan 24, 2009 (130)
25	1000GENOMES	ss113518111	Jan 25, 2009 (130)
26	ILLUMINA-UK	ss116873581	Feb 14, 2009 (130)
27	ENSEMBL	ss139387421	Dec 01, 2009 (131)
28	GMI	ss156225353	Dec 01, 2009 (131)
29	COMPLETE_GENOMICS	ss162809897	Jul 04, 2010 (132)
30	COMPLETE_GENOMICS	ss166021374	Jul 04, 2010 (132)
31	COMPLETE_GENOMICS	ss167270832	Jul 04, 2010 (132)
32	AFFY	ss173473061	Jul 04, 2010 (132)
33	BUSHMAN	ss201083012	Jul 04, 2010 (132)
34	BCM-HGSC-SUB	ss206982353	Jul 04, 2010 (132)
35	1000GENOMES	ss222062112	Jul 14, 2010 (132)
36	1000GENOMES	ss233216518	Jul 14, 2010 (132)
37	1000GENOMES	ss240325640	Jul 15, 2010 (132)
38	BL	ss253904894	May 09, 2011 (134)
39	GMI	ss278548486	May 04, 2012 (137)
40	GMI	ss285291295	Apr 25, 2013 (138)
41	PJP	ss293501877	May 09, 2011 (134)
42	TISHKOFF	ss558825247	Apr 25, 2013 (138)
43	SSMP	ss652730229	Apr 25, 2013 (138)
44	EVA-GONL	ss982305882	Aug 21, 2014 (142)
45	JMKIDD_LAB	ss1073177519	Aug 21, 2014 (142)
46	1000GENOMES	ss1317929206	Aug 21, 2014 (142)
47	DDI	ss1430554673	Apr 01, 2015 (144)
48	EVA_GENOME_DK	ss1581421341	Apr 01, 2015 (144)
49	EVA_DECODE	ss1591843389	Apr 01, 2015 (144)
50	EVA_UK10K_ALSPAC	ss1614397118	Apr 01, 2015 (144)
51	EVA_UK10K_TWINSUK	ss1657391151	Apr 01, 2015 (144)
52	EVA_SVP	ss1712814088	Apr 01, 2015 (144)
53	HAMMER_LAB	ss1804157525	Sep 08, 2015 (146)
54	WEILL_CORNELL_DGM	ss1925560361	Feb 12, 2016 (147)
55	GENOMED	ss1970248915	Jul 19, 2016 (147)
56	JJLAB	ss2023390132	Sep 14, 2016 (149)
57	USC_VALOUEV	ss2151549369	Dec 20, 2016 (150)
58	HUMAN_LONGEVITY	ss2279647739	Dec 20, 2016 (150)
59	SYSTEMSBIOZJU	ss2626183480	Nov 08, 2017 (151)
60	GRF	ss2707121421	Nov 08, 2017 (151)
61	GNOMAD	ss2832814268	Nov 08, 2017 (151)
62	SWEGEN	ss2998078659	Nov 08, 2017 (151)
63	BIOINF_KMB_FNS_UNIBA	ss3025477141	Nov 08, 2017 (151)
64	CSHL	ss3346706872	Nov 08, 2017 (151)
65	URBANLAB	ss3648206603	Oct 12, 2018 (152)
66	EGCUT_WGS	ss3666002527	Jul 13, 2019 (153)
67	EVA_DECODE	ss3716049605	Jul 13, 2019 (153)
68	ACPOP	ss3732967918	Jul 13, 2019 (153)
69	EVA	ss3764283453	Jul 13, 2019 (153)
70	PACBIO	ss3785298093	Jul 13, 2019 (153)
71	PACBIO	ss3790673516	Jul 13, 2019 (153)
72	PACBIO	ss3795550606	Jul 13, 2019 (153)
73	KHV_HUMAN_GENOMES	ss3807450168	Jul 13, 2019 (153)
74	EVA	ss3829592173	Apr 26, 2020 (154)
75	EVA	ss3838269560	Apr 26, 2020 (154)
76	EVA	ss3843712986	Apr 26, 2020 (154)
77	SGDP_PRJ	ss3863345426	Apr 26, 2020 (154)
78	KRGDB	ss3910032899	Apr 26, 2020 (154)
79	KOGIC	ss3957985850	Apr 26, 2020 (154)
80	TOPMED	ss4684929284	Apr 26, 2021 (155)
81	TOMMO_GENOMICS	ss5174948868	Apr 26, 2021 (155)
82	1000G_HIGH_COVERAGE	ss5266466164	Oct 13, 2022 (156)
83	EVA	ss5362111478	Oct 13, 2022 (156)
84	HUGCELL_USP	ss5464367047	Oct 13, 2022 (156)
85	EVA	ss5508274432	Oct 13, 2022 (156)
86	1000G_HIGH_COVERAGE	ss5551434395	Oct 13, 2022 (156)
87	SANFORD_IMAGENETICS	ss5639234508	Oct 13, 2022 (156)
88	TOMMO_GENOMICS	ss5712260090	Oct 13, 2022 (156)
89	YY_MCH	ss5806918115	Oct 13, 2022 (156)
90	EVA	ss5835884735	Oct 13, 2022 (156)
91	EVA	ss5855089565	Oct 13, 2022 (156)
92	EVA	ss5897046594	Oct 13, 2022 (156)
93	EVA	ss5967721129	Oct 13, 2022 (156)
94	1000Genomes	NC_000005.9 - 156624400	Oct 12, 2018 (152)
95	1000Genomes_30x	NC_000005.10 - 157197389	Oct 13, 2022 (156)
96	The Avon Longitudinal Study of Parents and Children	NC_000005.9 - 156624400	Oct 12, 2018 (152)
97	Genetic variation in the Estonian population	NC_000005.9 - 156624400	Oct 12, 2018 (152)
98	The Danish reference pan genome	NC_000005.9 - 156624400	Apr 26, 2020 (154)
99	gnomAD - Genomes	NC_000005.10 - 157197389	Apr 26, 2021 (155)
100	Genome of the Netherlands Release 5	NC_000005.9 - 156624400	Apr 26, 2020 (154)
101	HapMap	NC_000005.10 - 157197389	Apr 26, 2020 (154)
102	KOREAN population from KRGDB	NC_000005.9 - 156624400	Apr 26, 2020 (154)
103	Korean Genome Project	NC_000005.10 - 157197389	Apr 26, 2020 (154)
104	Northern Sweden	NC_000005.9 - 156624400	Jul 13, 2019 (153)
105	Qatari	NC_000005.9 - 156624400	Apr 26, 2020 (154)
106	SGDP_PRJ	NC_000005.9 - 156624400	Apr 26, 2020 (154)
107	Siberian	NC_000005.9 - 156624400	Apr 26, 2020 (154)
108	8.3KJPN	NC_000005.9 - 156624400	Apr 26, 2021 (155)
109	14KJPN	NC_000005.10 - 157197389	Oct 13, 2022 (156)
110	TopMed	NC_000005.10 - 157197389	Apr 26, 2021 (155)
111	UK 10K study - Twins	NC_000005.9 - 156624400	Oct 12, 2018 (152)
112	A Vietnamese Genetic Variation Database	NC_000005.9 - 156624400	Jul 13, 2019 (153)
113	ALFA	NC_000005.10 - 157197389	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)
rs56460855	May 25, 2008 (130)
rs58739391	Feb 26, 2009 (130)
rs59112311	May 25, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
15008200798	NC_000005.10:157197388:A:C	NC_000005.10:157197388:A:C	(self)
ss77280470, ss81302801, ss109546564, ss113518111, ss116873581, ss162809897, ss166021374, ss167270832, ss201083012, ss206982353, ss253904894, ss278548486, ss285291295, ss293501877, ss1591843389, ss1712814088	NC_000005.8:156556977:A:G	NC_000005.10:157197388:A:G	(self)
29632813, 16492676, 11740775, 7586280, 7320296, 17210293, 6252783, 7602291, 15362406, 4065723, 32918175, 16492676, 3655166, ss222062112, ss233216518, ss240325640, ss558825247, ss652730229, ss982305882, ss1073177519, ss1317929206, ss1430554673, ss1581421341, ss1614397118, ss1657391151, ss1804157525, ss1925560361, ss1970248915, ss2023390132, ss2151549369, ss2626183480, ss2707121421, ss2832814268, ss2998078659, ss3346706872, ss3666002527, ss3732967918, ss3764283453, ss3785298093, ss3790673516, ss3795550606, ss3829592173, ss3838269560, ss3863345426, ss3910032899, ss5174948868, ss5362111478, ss5508274432, ss5639234508, ss5835884735, ss5967721129	NC_000005.9:156624399:A:G	NC_000005.10:157197388:A:G	(self)
38960330, 209583179, 3005477, 14363851, 46097194, 522306841, 15008200798, ss2279647739, ss3025477141, ss3648206603, ss3716049605, ss3807450168, ss3843712986, ss3957985850, ss4684929284, ss5266466164, ss5464367047, ss5551434395, ss5712260090, ss5806918115, ss5855089565, ss5897046594	NC_000005.10:157197388:A:G	NC_000005.10:157197388:A:G	(self)
ss11731749, ss14814072, ss17858617, ss22291603	NT_023133.11:1433957:A:G	NC_000005.10:157197388:A:G	(self)
ss29973, ss31693, ss486580, ss1088398, ss1088790, ss1784560, ss1784726, ss1830774, ss5177290, ss5286468, ss5885505, ss6481691, ss66253132, ss76398509, ss81404749, ss98659375, ss104254886, ss139387421, ss156225353, ss173473061	NT_023133.13:1435672:A:G	NC_000005.10:157197388:A:G	(self)

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

2 citations for rs25855

PMID	Title	Author	Year	Journal
24867713	Association of T-cell immunoglobulin and mucin domain-containing molecule 3 (Tim-3) polymorphisms with susceptibility and disease progression of HBV infection.	Liao J et al.	2014	PloS one
30939292	Genetic association and interaction of PD1 and TIM3 polymorphisms in susceptibility of chronic hepatitis B virus infection and hepatocarcinogenesis.	Li F et al.	2019	Discovery medicine

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs25855