Name: rs2339474
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.

rs2339474

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:29781410 (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=0.063584 (16830/264690, TOPMED)
C=0.0532 (378/7102, ALFA)
C=0.0842 (539/6404, 1000G_30x) (+ 13 more)
C=0.0835 (418/5008, 1000G)
C=0.0502 (225/4480, Estonian)
C=0.0332 (128/3854, ALSPAC)
C=0.0318 (118/3708, TWINSUK)
C=0.0526 (154/2930, KOREAN)
C=0.027 (27/998, GoNL)
C=0.022 (13/600, NorthernSweden)
C=0.074 (40/544, SGDP_PRJ)
C=0.104 (34/328, HapMap)
C=0.051 (11/216, Qatari)
C=0.138 (29/210, Vietnamese)
C=0.02 (1/56, Siberian)
C=0.05 (2/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ALK : 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	7102	C=0.0532	A=0.0000, G=0.9468, T=0.0000
European	Sub	6676	C=0.0424	A=0.0000, G=0.9576, T=0.0000
African	Sub	190	C=0.395	A=0.000, G=0.605, T=0.000
African Others	Sub	8	C=0.5	A=0.0, G=0.5, T=0.0
African American	Sub	182	C=0.390	A=0.000, G=0.610, T=0.000
Asian	Sub	4	C=0.2	A=0.0, G=0.8, T=0.0
East Asian	Sub	2	C=0.5	A=0.0, G=0.5, T=0.0
Other Asian	Sub	2	C=0.0	A=0.0, G=1.0, T=0.0
Latin American 1	Sub	2	C=1.0	A=0.0, G=0.0, T=0.0
Latin American 2	Sub	0	C=0	A=0, G=0, T=0
South Asian	Sub	4	C=0.0	A=0.0, G=1.0, T=0.0
Other	Sub	226	C=0.075	A=0.000, G=0.925, T=0.000

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=0.063584	G=0.936416
Allele Frequency Aggregator	Total	Global	7102	C=0.0532	A=0.0000, G=0.9468, T=0.0000
Allele Frequency Aggregator	European	Sub	6676	C=0.0424	A=0.0000, G=0.9576, T=0.0000
Allele Frequency Aggregator	Other	Sub	226	C=0.075	A=0.000, G=0.925, T=0.000
Allele Frequency Aggregator	African	Sub	190	C=0.395	A=0.000, G=0.605, T=0.000
Allele Frequency Aggregator	South Asian	Sub	4	C=0.0	A=0.0, G=1.0, T=0.0
Allele Frequency Aggregator	Asian	Sub	4	C=0.2	A=0.0, G=0.8, T=0.0
Allele Frequency Aggregator	Latin American 1	Sub	2	C=1.0	A=0.0, G=0.0, T=0.0
Allele Frequency Aggregator	Latin American 2	Sub	0	C=0	A=0, G=0, T=0
1000Genomes_30x	Global	Study-wide	6404	C=0.0842	A=0.0003, G=0.9155
1000Genomes_30x	African	Sub	1786	C=0.1361	A=0.0000, G=0.8639
1000Genomes_30x	Europe	Sub	1266	C=0.0403	A=0.0000, G=0.9597
1000Genomes_30x	South Asian	Sub	1202	C=0.1140	A=0.0000, G=0.8860
1000Genomes_30x	East Asian	Sub	1170	C=0.0744	A=0.0000, G=0.9256
1000Genomes_30x	American	Sub	980	C=0.021	A=0.002, G=0.977
1000Genomes	Global	Study-wide	5008	C=0.0835	G=0.9165
1000Genomes	African	Sub	1322	C=0.1369	G=0.8631
1000Genomes	East Asian	Sub	1008	C=0.0744	G=0.9256
1000Genomes	Europe	Sub	1006	C=0.0388	G=0.9612
1000Genomes	South Asian	Sub	978	C=0.110	G=0.890
1000Genomes	American	Sub	694	C=0.022	G=0.978
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.0502	G=0.9498
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.0332	G=0.9668
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.0318	G=0.9682
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0526	A=0.0000, G=0.9474, T=0.0000
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.027	G=0.973
Northern Sweden	ACPOP	Study-wide	600	C=0.022	G=0.978
SGDP_PRJ	Global	Study-wide	544	C=0.074	G=0.926
HapMap	Global	Study-wide	328	C=0.104	G=0.896
HapMap	African	Sub	120	C=0.175	G=0.825
HapMap	American	Sub	120	C=0.067	G=0.933
HapMap	Asian	Sub	88	C=0.06	G=0.94
Qatari	Global	Study-wide	216	C=0.051	G=0.949
A Vietnamese Genetic Variation Database	Global	Study-wide	210	C=0.138	G=0.862
Siberian	Global	Study-wide	56	C=0.02	G=0.98
The Danish reference pan genome	Danish	Study-wide	40	C=0.05	G=0.95

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 2	NC_000002.12:g.29781410C>A
GRCh38.p14 chr 2	NC_000002.12:g.29781410C>G
GRCh38.p14 chr 2	NC_000002.12:g.29781410C>T
GRCh37.p13 chr 2	NC_000002.11:g.30004276C>A
GRCh37.p13 chr 2	NC_000002.11:g.30004276C>G
GRCh37.p13 chr 2	NC_000002.11:g.30004276C>T
ALK RefSeqGene (LRG_488)	NG_009445.1:g.145157G>T
ALK RefSeqGene (LRG_488)	NG_009445.1:g.145157G>C
ALK RefSeqGene (LRG_488)	NG_009445.1:g.145157G>A

Gene: ALK, ALK receptor tyrosine kinase (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ALK transcript variant 1	NM_004304.5:c.668-63713G>T	N/A	Intron Variant
ALK transcript variant 2	NM_001353765.2:c.	N/A	Genic Upstream Transcript Variant
ALK transcript variant X1	XR_001738688.3:n.	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	C=	A	G	T
GRCh38.p14 chr 2	NC_000002.12:g.29781410=	NC_000002.12:g.29781410C>A	NC_000002.12:g.29781410C>G	NC_000002.12:g.29781410C>T
GRCh37.p13 chr 2	NC_000002.11:g.30004276=	NC_000002.11:g.30004276C>A	NC_000002.11:g.30004276C>G	NC_000002.11:g.30004276C>T
ALK RefSeqGene (LRG_488)	NG_009445.1:g.145157=	NG_009445.1:g.145157G>T	NG_009445.1:g.145157G>C	NG_009445.1:g.145157G>A
ALK transcript variant 1	NM_004304.4:c.668-63713=	NM_004304.4:c.668-63713G>T	NM_004304.4:c.668-63713G>C	NM_004304.4:c.668-63713G>A
ALK transcript variant 1	NM_004304.5:c.668-63713=	NM_004304.5:c.668-63713G>T	NM_004304.5:c.668-63713G>C	NM_004304.5:c.668-63713G>A

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#.

81 SubSNP, 24 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss3292459	Sep 28, 2001 (100)
2	SSAHASNP	ss21625151	Apr 05, 2004 (121)
3	ABI	ss44211845	Mar 13, 2006 (126)
4	HGSV	ss77292268	Dec 06, 2007 (129)
5	BCMHGSC_JDW	ss91102498	Mar 24, 2008 (129)
6	HUMANGENOME_JCVI	ss96384649	Feb 02, 2009 (130)
7	BGI	ss106078278	Feb 02, 2009 (130)
8	1000GENOMES	ss109364569	Jan 24, 2009 (130)
9	1000GENOMES	ss110008836	Jan 24, 2009 (130)
10	ILLUMINA-UK	ss117638644	Feb 14, 2009 (130)
11	ENSEMBL	ss135904840	Dec 01, 2009 (131)
12	ENSEMBL	ss138412847	Dec 01, 2009 (131)
13	GMI	ss156851787	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss163238447	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss164081560	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss166345651	Jul 04, 2010 (132)
17	BUSHMAN	ss200213102	Jul 04, 2010 (132)
18	BCM-HGSC-SUB	ss205742615	Jul 04, 2010 (132)
19	1000GENOMES	ss219143254	Jul 14, 2010 (132)
20	1000GENOMES	ss231092740	Jul 14, 2010 (132)
21	1000GENOMES	ss238664594	Jul 15, 2010 (132)
22	BL	ss253000527	May 09, 2011 (134)
23	GMI	ss276400102	May 04, 2012 (137)
24	GMI	ss284315772	Apr 25, 2013 (138)
25	PJP	ss292535217	May 09, 2011 (134)
26	TISHKOFF	ss555443071	Apr 25, 2013 (138)
27	SSMP	ss649023484	Apr 25, 2013 (138)
28	EVA-GONL	ss976631462	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1068965029	Aug 21, 2014 (142)
30	1000GENOMES	ss1296462163	Aug 21, 2014 (142)
31	DDI	ss1428519633	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1578797331	Apr 01, 2015 (144)
33	EVA_DECODE	ss1586037434	Apr 01, 2015 (144)
34	EVA_UK10K_ALSPAC	ss1603104024	Apr 01, 2015 (144)
35	EVA_UK10K_TWINSUK	ss1646098057	Apr 01, 2015 (144)
36	HAMMER_LAB	ss1796479178	Sep 08, 2015 (146)
37	WEILL_CORNELL_DGM	ss1919863918	Feb 12, 2016 (147)
38	GENOMED	ss1968725463	Jul 19, 2016 (147)
39	JJLAB	ss2020460911	Sep 14, 2016 (149)
40	USC_VALOUEV	ss2148505193	Dec 20, 2016 (150)
41	HUMAN_LONGEVITY	ss2228667458	Dec 20, 2016 (150)
42	SYSTEMSBIOZJU	ss2624745159	Nov 08, 2017 (151)
43	GRF	ss2703066144	Nov 08, 2017 (151)
44	GNOMAD	ss2771287443	Nov 08, 2017 (151)
45	AFFY	ss2985788762	Nov 08, 2017 (151)
46	SWEGEN	ss2989199102	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3023996992	Nov 08, 2017 (151)
48	CSHL	ss3344137848	Nov 08, 2017 (151)
49	URBANLAB	ss3646994881	Oct 11, 2018 (152)
50	EGCUT_WGS	ss3657154794	Jul 13, 2019 (153)
51	EVA_DECODE	ss3703521493	Jul 13, 2019 (153)
52	ACPOP	ss3728270894	Jul 13, 2019 (153)
53	EVA	ss3756524311	Jul 13, 2019 (153)
54	PACBIO	ss3783815980	Jul 13, 2019 (153)
55	PACBIO	ss3789411199	Jul 13, 2019 (153)
56	PACBIO	ss3794283975	Jul 13, 2019 (153)
57	KHV_HUMAN_GENOMES	ss3800903129	Jul 13, 2019 (153)
58	EVA	ss3826889358	Apr 25, 2020 (154)
59	EVA	ss3836851997	Apr 25, 2020 (154)
60	EVA	ss3842266683	Apr 25, 2020 (154)
61	SGDP_PRJ	ss3851876435	Apr 25, 2020 (154)
62	KRGDB	ss3897294497	Apr 25, 2020 (154)
63	KOGIC	ss3947387977	Apr 25, 2020 (154)
64	KOGIC	ss3947387978	Apr 25, 2020 (154)
65	TOPMED	ss4498949557	Apr 26, 2021 (155)
66	TOMMO_GENOMICS	ss5150493033	Apr 26, 2021 (155)
67	TOMMO_GENOMICS	ss5150493034	Apr 26, 2021 (155)
68	1000G_HIGH_COVERAGE	ss5247395839	Oct 17, 2022 (156)
69	1000G_HIGH_COVERAGE	ss5247395840	Oct 17, 2022 (156)
70	EVA	ss5327701446	Oct 17, 2022 (156)
71	HUGCELL_USP	ss5447660357	Oct 17, 2022 (156)
72	1000G_HIGH_COVERAGE	ss5522263478	Oct 17, 2022 (156)
73	SANFORD_IMAGENETICS	ss5628364928	Oct 17, 2022 (156)
74	TOMMO_GENOMICS	ss5678866862	Oct 17, 2022 (156)
75	TOMMO_GENOMICS	ss5678866863	Oct 17, 2022 (156)
76	YY_MCH	ss5802041762	Oct 17, 2022 (156)
77	EVA	ss5819841149	Oct 17, 2022 (156)
78	EVA	ss5852446046	Oct 17, 2022 (156)
79	EVA	ss5929586734	Oct 17, 2022 (156)
80	EVA	ss5954569799	Oct 17, 2022 (156)
81	EVA	ss5980045955	Oct 17, 2022 (156)
82	1000Genomes	NC_000002.11 - 30004276	Oct 11, 2018 (152)
83	1000Genomes_30x	NC_000002.12 - 29781410	Oct 17, 2022 (156)
84	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 30004276	Oct 11, 2018 (152)
85	Genetic variation in the Estonian population	NC_000002.11 - 30004276	Oct 11, 2018 (152)
86	The Danish reference pan genome	NC_000002.11 - 30004276	Apr 25, 2020 (154)
87	gnomAD - Genomes Submission ignored due to conflicting rows: Row 52454703 (NC_000002.12:29781409:C:A 5/140192) Row 52454704 (NC_000002.12:29781409:C:G 131401/140174)	-	Apr 26, 2021 (155)
88	gnomAD - Genomes Submission ignored due to conflicting rows: Row 52454703 (NC_000002.12:29781409:C:A 5/140192) Row 52454704 (NC_000002.12:29781409:C:G 131401/140174)	-	Apr 26, 2021 (155)
89	Genome of the Netherlands Release 5	NC_000002.11 - 30004276	Apr 25, 2020 (154)
90	HapMap	NC_000002.12 - 29781410	Apr 25, 2020 (154)
91	KOREAN population from KRGDB	NC_000002.11 - 30004276	Apr 25, 2020 (154)
92	Korean Genome Project Submission ignored due to conflicting rows: Row 3765978 (NC_000002.12:29781409:C:G 1747/1832) Row 3765979 (NC_000002.12:29781409:C:A 1/1832)	-	Apr 25, 2020 (154)
93	Korean Genome Project Submission ignored due to conflicting rows: Row 3765978 (NC_000002.12:29781409:C:G 1747/1832) Row 3765979 (NC_000002.12:29781409:C:A 1/1832)	-	Apr 25, 2020 (154)
94	Northern Sweden	NC_000002.11 - 30004276	Jul 13, 2019 (153)
95	Qatari	NC_000002.11 - 30004276	Apr 25, 2020 (154)
96	SGDP_PRJ	NC_000002.11 - 30004276	Apr 25, 2020 (154)
97	Siberian	NC_000002.11 - 30004276	Apr 25, 2020 (154)
98	8.3KJPN Submission ignored due to conflicting rows: Row 8462340 (NC_000002.11:30004275:C:G 15979/16760) Row 8462341 (NC_000002.11:30004275:C:A 2/16760)	-	Apr 26, 2021 (155)
99	8.3KJPN Submission ignored due to conflicting rows: Row 8462340 (NC_000002.11:30004275:C:G 15979/16760) Row 8462341 (NC_000002.11:30004275:C:A 2/16760)	-	Apr 26, 2021 (155)
100	14KJPN Submission ignored due to conflicting rows: Row 12703966 (NC_000002.12:29781409:C:G 26967/28258) Row 12703967 (NC_000002.12:29781409:C:A 5/28258)	-	Oct 17, 2022 (156)
101	14KJPN Submission ignored due to conflicting rows: Row 12703966 (NC_000002.12:29781409:C:G 26967/28258) Row 12703967 (NC_000002.12:29781409:C:A 5/28258)	-	Oct 17, 2022 (156)
102	TopMed	NC_000002.12 - 29781410	Apr 26, 2021 (155)
103	UK 10K study - Twins	NC_000002.11 - 30004276	Oct 11, 2018 (152)
104	A Vietnamese Genetic Variation Database	NC_000002.11 - 30004276	Jul 13, 2019 (153)
105	ALFA	NC_000002.12 - 29781410	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
4471891, ss3897294497, ss5150493034	NC_000002.11:30004275:C:A	NC_000002.12:29781409:C:A	(self)
9789413, 3794214549, ss2228667458, ss3947387978, ss5247395840, ss5522263478, ss5678866863	NC_000002.12:29781409:C:A	NC_000002.12:29781409:C:A	(self)
ss77292268	NC_000002.9:29915926:C:G	NC_000002.12:29781409:C:G	(self)
ss91102498, ss109364569, ss110008836, ss117638644, ss163238447, ss164081560, ss166345651, ss200213102, ss205742615, ss253000527, ss276400102, ss284315772, ss292535217, ss1586037434	NC_000002.10:29857779:C:G	NC_000002.12:29781409:C:G	(self)
7382847, 4099491, 2893042, 4973137, 1800350, 4471891, 1555759, 1905848, 3893415, 1021547, 4099491, 892389, ss219143254, ss231092740, ss238664594, ss555443071, ss649023484, ss976631462, ss1068965029, ss1296462163, ss1428519633, ss1578797331, ss1603104024, ss1646098057, ss1796479178, ss1919863918, ss1968725463, ss2020460911, ss2148505193, ss2624745159, ss2703066144, ss2771287443, ss2985788762, ss2989199102, ss3344137848, ss3657154794, ss3728270894, ss3756524311, ss3783815980, ss3789411199, ss3794283975, ss3826889358, ss3836851997, ss3851876435, ss3897294497, ss5150493033, ss5327701446, ss5628364928, ss5819841149, ss5954569799, ss5980045955	NC_000002.11:30004275:C:G	NC_000002.12:29781409:C:G	(self)
9789413, 1761853, 302772436, 3794214549, ss2228667458, ss3023996992, ss3646994881, ss3703521493, ss3800903129, ss3842266683, ss3947387977, ss4498949557, ss5247395839, ss5447660357, ss5522263478, ss5678866862, ss5802041762, ss5852446046, ss5929586734	NC_000002.12:29781409:C:G	NC_000002.12:29781409:C:G	(self)
ss21625151	NT_022184.13:8820208:C:G	NC_000002.12:29781409:C:G	(self)
ss3292459, ss44211845, ss96384649, ss106078278, ss135904840, ss138412847, ss156851787	NT_022184.15:8826162:C:G	NC_000002.12:29781409:C:G	(self)
4471891, ss3897294497	NC_000002.11:30004275:C:T	NC_000002.12:29781409:C:T	(self)
3794214549	NC_000002.12:29781409:C:T	NC_000002.12:29781409:C: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 rs2339474

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

rs2339474