Name: rs2345389
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.

rs2345389

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr16:66726563 (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: C=0.301598 (79830/264690, TOPMED)
G=0.38064 (10756/28258, 14KJPN)
G=0.38323 (6423/16760, 8.3KJPN) (+ 16 more)
C=0.17470 (2292/13120, ALFA)
C=0.3351 (2146/6404, 1000G_30x)
C=0.3442 (1724/5008, 1000G)
C=0.3219 (1442/4480, Estonian)
C=0.3290 (1268/3854, ALSPAC)
C=0.3242 (1202/3708, TWINSUK)
G=0.3539 (1037/2930, KOREAN)
G=0.3772 (691/1832, Korea1K)
C=0.364 (363/998, GoNL)
C=0.288 (173/600, NorthernSweden)
G=0.311 (107/344, SGDP_PRJ)
C=0.330 (105/318, HapMap)
C=0.380 (82/216, Qatari)
G=0.426 (92/216, Vietnamese)
C=0.35 (14/40, GENOME_DK)
G=0.32 (12/38, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DYNC1LI2 : 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	13120	G=0.82530	A=0.00000, C=0.17470, T=0.00000
European	Sub	10068	G=0.78178	A=0.00000, C=0.21822, T=0.00000
African	Sub	2336	G=0.9953	A=0.0000, C=0.0047, T=0.0000
African Others	Sub	94	G=1.00	A=0.00, C=0.00, T=0.00
African American	Sub	2242	G=0.9951	A=0.0000, C=0.0049, T=0.0000
Asian	Sub	10	G=0.8	A=0.0, C=0.2, T=0.0
East Asian	Sub	6	G=0.8	A=0.0, C=0.2, T=0.0
Other Asian	Sub	4	G=0.8	A=0.0, C=0.2, T=0.0
Latin American 1	Sub	82	G=1.00	A=0.00, C=0.00, T=0.00
Latin American 2	Sub	150	G=1.000	A=0.000, C=0.000, T=0.000
South Asian	Sub	38	G=0.97	A=0.00, C=0.03, T=0.00
Other	Sub	436	G=0.814	A=0.000, C=0.186, 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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.698402	C=0.301598
14KJPN	JAPANESE	Study-wide	28258	G=0.38064	C=0.61936
8.3KJPN	JAPANESE	Study-wide	16760	G=0.38323	C=0.61677
Allele Frequency Aggregator	Total	Global	13120	G=0.82530	A=0.00000, C=0.17470, T=0.00000
Allele Frequency Aggregator	European	Sub	10068	G=0.78178	A=0.00000, C=0.21822, T=0.00000
Allele Frequency Aggregator	African	Sub	2336	G=0.9953	A=0.0000, C=0.0047, T=0.0000
Allele Frequency Aggregator	Other	Sub	436	G=0.814	A=0.000, C=0.186, T=0.000
Allele Frequency Aggregator	Latin American 2	Sub	150	G=1.000	A=0.000, C=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	82	G=1.00	A=0.00, C=0.00, T=0.00
Allele Frequency Aggregator	South Asian	Sub	38	G=0.97	A=0.00, C=0.03, T=0.00
Allele Frequency Aggregator	Asian	Sub	10	G=0.8	A=0.0, C=0.2, T=0.0
1000Genomes_30x	Global	Study-wide	6404	G=0.6649	C=0.3351
1000Genomes_30x	African	Sub	1786	G=0.9334	C=0.0666
1000Genomes_30x	Europe	Sub	1266	G=0.6517	C=0.3483
1000Genomes_30x	South Asian	Sub	1202	G=0.6073	C=0.3927
1000Genomes_30x	East Asian	Sub	1170	G=0.3872	C=0.6128
1000Genomes_30x	American	Sub	980	G=0.595	C=0.405
1000Genomes	Global	Study-wide	5008	G=0.6558	C=0.3442
1000Genomes	African	Sub	1322	G=0.9312	C=0.0688
1000Genomes	East Asian	Sub	1008	G=0.3829	C=0.6171
1000Genomes	Europe	Sub	1006	G=0.6511	C=0.3489
1000Genomes	South Asian	Sub	978	G=0.606	C=0.394
1000Genomes	American	Sub	694	G=0.604	C=0.396
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.6781	C=0.3219
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.6710	C=0.3290
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.6758	C=0.3242
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.3539	A=0.0000, C=0.6461, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	G=0.3772	C=0.6228
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.636	C=0.364
Northern Sweden	ACPOP	Study-wide	600	G=0.712	C=0.288
SGDP_PRJ	Global	Study-wide	344	G=0.311	C=0.689
HapMap	Global	Study-wide	318	G=0.670	C=0.330
HapMap	American	Sub	116	G=0.638	C=0.362
HapMap	African	Sub	112	G=0.920	C=0.080
HapMap	Asian	Sub	90	G=0.40	C=0.60
Qatari	Global	Study-wide	216	G=0.620	C=0.380
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.426	C=0.574
The Danish reference pan genome	Danish	Study-wide	40	G=0.65	C=0.35
Siberian	Global	Study-wide	38	G=0.32	C=0.68

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 16	NC_000016.10:g.66726563G>A
GRCh38.p14 chr 16	NC_000016.10:g.66726563G>C
GRCh38.p14 chr 16	NC_000016.10:g.66726563G>T
GRCh37.p13 chr 16	NC_000016.9:g.66760466G>A
GRCh37.p13 chr 16	NC_000016.9:g.66760466G>C
GRCh37.p13 chr 16	NC_000016.9:g.66760466G>T

Gene: DYNC1LI2, dynein cytoplasmic 1 light intermediate chain 2 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DYNC1LI2 transcript variant 2	NM_001286157.2:c.1031-619… NM_001286157.2:c.1031-619C>T	N/A	Intron Variant
DYNC1LI2 transcript variant 3	NM_001323955.2:c.1145-619… NM_001323955.2:c.1145-619C>T	N/A	Intron Variant
DYNC1LI2 transcript variant 1	NM_006141.3:c.1262-619C>T	N/A	Intron Variant
DYNC1LI2 transcript variant 4	NR_136658.2:n.	N/A	Intron Variant
DYNC1LI2 transcript variant X1	XM_017023008.2:c.1262-619… XM_017023008.2:c.1262-619C>T	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	G=	A	C	T
GRCh38.p14 chr 16	NC_000016.10:g.66726563=	NC_000016.10:g.66726563G>A	NC_000016.10:g.66726563G>C	NC_000016.10:g.66726563G>T
GRCh37.p13 chr 16	NC_000016.9:g.66760466=	NC_000016.9:g.66760466G>A	NC_000016.9:g.66760466G>C	NC_000016.9:g.66760466G>T
DYNC1LI2 transcript variant 2	NM_001286157.2:c.1031-619=	NM_001286157.2:c.1031-619C>T	NM_001286157.2:c.1031-619C>G	NM_001286157.2:c.1031-619C>A
DYNC1LI2 transcript variant 3	NM_001323955.2:c.1145-619=	NM_001323955.2:c.1145-619C>T	NM_001323955.2:c.1145-619C>G	NM_001323955.2:c.1145-619C>A
DYNC1LI2 transcript variant 1	NM_006141.2:c.1262-619=	NM_006141.2:c.1262-619C>T	NM_006141.2:c.1262-619C>G	NM_006141.2:c.1262-619C>A
DYNC1LI2 transcript variant 1	NM_006141.3:c.1262-619=	NM_006141.3:c.1262-619C>T	NM_006141.3:c.1262-619C>G	NM_006141.3:c.1262-619C>A
DYNC1LI2 transcript variant X1	XM_005255831.1:c.1031-619=	XM_005255831.1:c.1031-619C>T	XM_005255831.1:c.1031-619C>G	XM_005255831.1:c.1031-619C>A
DYNC1LI2 transcript variant X1	XM_017023008.2:c.1262-619=	XM_017023008.2:c.1262-619C>T	XM_017023008.2:c.1262-619C>G	XM_017023008.2:c.1262-619C>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#.

63 SubSNP, 22 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss3299356	Sep 28, 2001 (100)
2	SC_JCM	ss6219935	Feb 20, 2003 (111)
3	SSAHASNP	ss21310062	Apr 05, 2004 (121)
4	ABI	ss40721081	Mar 13, 2006 (126)
5	HGSV	ss77502442	Dec 07, 2007 (129)
6	HUMANGENOME_JCVI	ss96643434	Feb 05, 2009 (130)
7	ILLUMINA-UK	ss118288984	Dec 01, 2009 (131)
8	ENSEMBL	ss136704793	Dec 01, 2009 (131)
9	GMI	ss157473670	Dec 01, 2009 (131)
10	COMPLETE_GENOMICS	ss168371666	Jul 04, 2010 (132)
11	COMPLETE_GENOMICS	ss171372583	Jul 04, 2010 (132)
12	1000GENOMES	ss227298752	Jul 14, 2010 (132)
13	1000GENOMES	ss237066201	Jul 15, 2010 (132)
14	1000GENOMES	ss243398022	Jul 15, 2010 (132)
15	BL	ss255776651	May 09, 2011 (134)
16	GMI	ss282573263	May 04, 2012 (137)
17	PJP	ss291862646	May 09, 2011 (134)
18	TISHKOFF	ss564966081	Apr 25, 2013 (138)
19	SSMP	ss660742881	Apr 25, 2013 (138)
20	EVA-GONL	ss992601252	Aug 21, 2014 (142)
21	JMKIDD_LAB	ss1080705665	Aug 21, 2014 (142)
22	1000GENOMES	ss1356666200	Aug 21, 2014 (142)
23	DDI	ss1427879440	Apr 01, 2015 (144)
24	EVA_GENOME_DK	ss1577958392	Apr 01, 2015 (144)
25	EVA_UK10K_ALSPAC	ss1634647813	Apr 01, 2015 (144)
26	EVA_UK10K_TWINSUK	ss1677641846	Apr 01, 2015 (144)
27	EVA_DECODE	ss1696636016	Apr 01, 2015 (144)
28	WEILL_CORNELL_DGM	ss1936032327	Feb 12, 2016 (147)
29	GENOMED	ss1968286755	Jul 19, 2016 (147)
30	JJLAB	ss2028802175	Sep 14, 2016 (149)
31	USC_VALOUEV	ss2157239605	Dec 20, 2016 (150)
32	HUMAN_LONGEVITY	ss2213032083	Dec 20, 2016 (150)
33	SYSTEMSBIOZJU	ss2628892360	Nov 08, 2017 (151)
34	GRF	ss2701768169	Nov 08, 2017 (151)
35	GNOMAD	ss2944204169	Nov 08, 2017 (151)
36	SWEGEN	ss3014683157	Nov 08, 2017 (151)
37	BIOINF_KMB_FNS_UNIBA	ss3028219462	Nov 08, 2017 (151)
38	CSHL	ss3351500208	Nov 08, 2017 (151)
39	URBANLAB	ss3650532074	Oct 12, 2018 (152)
40	EGCUT_WGS	ss3681666698	Jul 13, 2019 (153)
41	EVA_DECODE	ss3699473326	Jul 13, 2019 (153)
42	ACPOP	ss3741603721	Jul 13, 2019 (153)
43	EVA	ss3754067434	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3819351566	Jul 13, 2019 (153)
45	EVA	ss3834623350	Apr 27, 2020 (154)
46	SGDP_PRJ	ss3884659965	Apr 27, 2020 (154)
47	KRGDB	ss3934167673	Apr 27, 2020 (154)
48	KOGIC	ss3977792045	Apr 27, 2020 (154)
49	TOPMED	ss5019076304	Apr 26, 2021 (155)
50	TOMMO_GENOMICS	ss5220052986	Apr 26, 2021 (155)
51	1000G_HIGH_COVERAGE	ss5301328174	Oct 16, 2022 (156)
52	EVA	ss5424394991	Oct 16, 2022 (156)
53	HUGCELL_USP	ss5494645298	Oct 16, 2022 (156)
54	EVA	ss5511643986	Oct 16, 2022 (156)
55	1000G_HIGH_COVERAGE	ss5604172815	Oct 16, 2022 (156)
56	SANFORD_IMAGENETICS	ss5659112841	Oct 16, 2022 (156)
57	TOMMO_GENOMICS	ss5775198541	Oct 16, 2022 (156)
58	YY_MCH	ss5816064917	Oct 16, 2022 (156)
59	EVA	ss5846552781	Oct 16, 2022 (156)
60	EVA	ss5851611889	Oct 16, 2022 (156)
61	EVA	ss5899523338	Oct 16, 2022 (156)
62	EVA	ss5950512342	Oct 16, 2022 (156)
63	EVA	ss5980926746	Oct 16, 2022 (156)
64	1000Genomes	NC_000016.9 - 66760466	Oct 12, 2018 (152)
65	1000Genomes_30x	NC_000016.10 - 66726563	Oct 16, 2022 (156)
66	The Avon Longitudinal Study of Parents and Children	NC_000016.9 - 66760466	Oct 12, 2018 (152)
67	Genetic variation in the Estonian population	NC_000016.9 - 66760466	Oct 12, 2018 (152)
68	The Danish reference pan genome	NC_000016.9 - 66760466	Apr 27, 2020 (154)
69	gnomAD - Genomes Submission ignored due to conflicting rows: Row 492639408 (NC_000016.10:66726562:G:A 16/140180) Row 492639409 (NC_000016.10:66726562:G:C 40559/140162) Row 492639410 (NC_000016.10:66726562:G:T 1/140180)	-	Apr 26, 2021 (155)
70	gnomAD - Genomes Submission ignored due to conflicting rows: Row 492639408 (NC_000016.10:66726562:G:A 16/140180) Row 492639409 (NC_000016.10:66726562:G:C 40559/140162) Row 492639410 (NC_000016.10:66726562:G:T 1/140180)	-	Apr 26, 2021 (155)
71	gnomAD - Genomes Submission ignored due to conflicting rows: Row 492639408 (NC_000016.10:66726562:G:A 16/140180) Row 492639409 (NC_000016.10:66726562:G:C 40559/140162) Row 492639410 (NC_000016.10:66726562:G:T 1/140180)	-	Apr 26, 2021 (155)
72	Genome of the Netherlands Release 5	NC_000016.9 - 66760466	Apr 27, 2020 (154)
73	HapMap	NC_000016.10 - 66726563	Apr 27, 2020 (154)
74	KOREAN population from KRGDB	NC_000016.9 - 66760466	Apr 27, 2020 (154)
75	Korean Genome Project	NC_000016.10 - 66726563	Apr 27, 2020 (154)
76	Northern Sweden	NC_000016.9 - 66760466	Jul 13, 2019 (153)
77	Qatari	NC_000016.9 - 66760466	Apr 27, 2020 (154)
78	SGDP_PRJ	NC_000016.9 - 66760466	Apr 27, 2020 (154)
79	Siberian	NC_000016.9 - 66760466	Apr 27, 2020 (154)
80	8.3KJPN	NC_000016.9 - 66760466	Apr 26, 2021 (155)
81	14KJPN	NC_000016.10 - 66726563	Oct 16, 2022 (156)
82	TopMed	NC_000016.10 - 66726563	Apr 26, 2021 (155)
83	UK 10K study - Twins	NC_000016.9 - 66760466	Oct 12, 2018 (152)
84	A Vietnamese Genetic Variation Database	NC_000016.9 - 66760466	Jul 13, 2019 (153)
85	ALFA	NC_000016.10 - 66726563	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
41345067, ss2944204169, ss3934167673	NC_000016.9:66760465:G:A	NC_000016.10:66726562:G:A	(self)
13796588587, ss2213032083	NC_000016.10:66726562:G:A	NC_000016.10:66726562:G:A	(self)
ss77502442, ss118288984, ss168371666, ss171372583, ss255776651, ss282573263, ss291862646, ss1696636016	NC_000016.8:65317966:G:C	NC_000016.10:66726562:G:C	(self)
69844093, 38746891, 27404946, 4168972, 17278542, 41345067, 14888586, 18074249, 36676945, 9755959, 78022293, 38746891, 8595744, ss227298752, ss237066201, ss243398022, ss564966081, ss660742881, ss992601252, ss1080705665, ss1356666200, ss1427879440, ss1577958392, ss1634647813, ss1677641846, ss1936032327, ss1968286755, ss2028802175, ss2157239605, ss2628892360, ss2701768169, ss2944204169, ss3014683157, ss3351500208, ss3681666698, ss3741603721, ss3754067434, ss3834623350, ss3884659965, ss3934167673, ss5220052986, ss5424394991, ss5511643986, ss5659112841, ss5846552781, ss5950512342, ss5980926746	NC_000016.9:66760465:G:C	NC_000016.10:66726562:G:C	(self)
91698750, 1403034, 34170046, 109035645, 234621965, 13796588587, ss2213032083, ss3028219462, ss3650532074, ss3699473326, ss3819351566, ss3977792045, ss5019076304, ss5301328174, ss5494645298, ss5604172815, ss5775198541, ss5816064917, ss5851611889, ss5899523338	NC_000016.10:66726562:G:C	NC_000016.10:66726562:G:C	(self)
ss21310062	NT_010498.14:15482018:G:C	NC_000016.10:66726562:G:C	(self)
ss3299356, ss6219935, ss40721081, ss96643434, ss136704793, ss157473670	NT_010498.15:20374664:G:C	NC_000016.10:66726562:G:C	(self)
41345067, ss3934167673	NC_000016.9:66760465:G:T	NC_000016.10:66726562:G:T	(self)
13796588587	NC_000016.10:66726562:G:T	NC_000016.10:66726562: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 rs2345389

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

rs2345389