Name: rs12727390
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.

rs12727390

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:66769562 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.118006 (31235/264690, TOPMED)
T=0.117158 (16393/139922, GnomAD)
T=0.14700 (4154/28258, 14KJPN) (+ 18 more)
T=0.11721 (2141/18266, ALFA)
T=0.14445 (2421/16760, 8.3KJPN)
T=0.1299 (832/6404, 1000G_30x)
T=0.1330 (666/5008, 1000G)
T=0.1094 (490/4480, Estonian)
T=0.1209 (466/3854, ALSPAC)
T=0.1321 (490/3708, TWINSUK)
T=0.1468 (430/2930, KOREAN)
T=0.1392 (255/1832, Korea1K)
T=0.141 (141/998, GoNL)
T=0.070 (42/600, NorthernSweden)
T=0.100 (29/290, HapMap)
T=0.130 (28/216, Qatari)
T=0.198 (42/212, Vietnamese)
C=0.466 (54/116, SGDP_PRJ)
T=0.15 (6/40, GENOME_DK)
C=0.50 (8/16, Siberian)
T=0.50 (8/16, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: DYNLT5 : 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	18266	C=0.88279	A=0.00000, T=0.11721
European	Sub	13990	C=0.87155	A=0.00000, T=0.12845
African	Sub	2808	C=0.9352	A=0.0000, T=0.0648
African Others	Sub	114	C=0.939	A=0.000, T=0.061
African American	Sub	2694	C=0.9350	A=0.0000, T=0.0650
Asian	Sub	112	C=0.848	A=0.000, T=0.152
East Asian	Sub	86	C=0.83	A=0.00, T=0.17
Other Asian	Sub	26	C=0.92	A=0.00, T=0.08
Latin American 1	Sub	146	C=0.897	A=0.000, T=0.103
Latin American 2	Sub	610	C=0.918	A=0.000, T=0.082
South Asian	Sub	98	C=0.89	A=0.00, T=0.11
Other	Sub	502	C=0.863	A=0.000, T=0.137

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=0.881994	T=0.118006
gnomAD - Genomes	Global	Study-wide	139922	C=0.882842	T=0.117158
gnomAD - Genomes	European	Sub	75790	C=0.86831	T=0.13169
gnomAD - Genomes	African	Sub	41938	C=0.91430	T=0.08570
gnomAD - Genomes	American	Sub	13606	C=0.88608	T=0.11392
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	C=0.8232	T=0.1768
gnomAD - Genomes	East Asian	Sub	3122	C=0.8645	T=0.1355
gnomAD - Genomes	Other	Sub	2146	C=0.8798	T=0.1202
14KJPN	JAPANESE	Study-wide	28258	C=0.85300	T=0.14700
Allele Frequency Aggregator	Total	Global	18266	C=0.88279	A=0.00000, T=0.11721
Allele Frequency Aggregator	European	Sub	13990	C=0.87155	A=0.00000, T=0.12845
Allele Frequency Aggregator	African	Sub	2808	C=0.9352	A=0.0000, T=0.0648
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.918	A=0.000, T=0.082
Allele Frequency Aggregator	Other	Sub	502	C=0.863	A=0.000, T=0.137
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.897	A=0.000, T=0.103
Allele Frequency Aggregator	Asian	Sub	112	C=0.848	A=0.000, T=0.152
Allele Frequency Aggregator	South Asian	Sub	98	C=0.89	A=0.00, T=0.11
8.3KJPN	JAPANESE	Study-wide	16760	C=0.85555	T=0.14445
1000Genomes_30x	Global	Study-wide	6404	C=0.8701	T=0.1299
1000Genomes_30x	African	Sub	1786	C=0.9110	T=0.0890
1000Genomes_30x	Europe	Sub	1266	C=0.8491	T=0.1509
1000Genomes_30x	South Asian	Sub	1202	C=0.8186	T=0.1814
1000Genomes_30x	East Asian	Sub	1170	C=0.8487	T=0.1513
1000Genomes_30x	American	Sub	980	C=0.911	T=0.089
1000Genomes	Global	Study-wide	5008	C=0.8670	T=0.1330
1000Genomes	African	Sub	1322	C=0.9130	T=0.0870
1000Genomes	East Asian	Sub	1008	C=0.8512	T=0.1488
1000Genomes	Europe	Sub	1006	C=0.8489	T=0.1511
1000Genomes	South Asian	Sub	978	C=0.818	T=0.182
1000Genomes	American	Sub	694	C=0.898	T=0.102
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.8906	T=0.1094
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.8791	T=0.1209
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.8679	T=0.1321
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.8532	T=0.1468
Korean Genome Project	KOREAN	Study-wide	1832	C=0.8608	T=0.1392
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.859	T=0.141
Northern Sweden	ACPOP	Study-wide	600	C=0.930	T=0.070
HapMap	Global	Study-wide	290	C=0.900	T=0.100
HapMap	African	Sub	106	C=0.981	T=0.019
HapMap	American	Sub	106	C=0.858	T=0.142
HapMap	Asian	Sub	78	C=0.85	T=0.15
Qatari	Global	Study-wide	216	C=0.870	T=0.130
A Vietnamese Genetic Variation Database	Global	Study-wide	212	C=0.802	T=0.198
SGDP_PRJ	Global	Study-wide	116	C=0.466	T=0.534
The Danish reference pan genome	Danish	Study-wide	40	C=0.85	T=0.15
Siberian	Global	Study-wide	16	C=0.50	T=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 1	NC_000001.11:g.66769562C>A
GRCh38.p14 chr 1	NC_000001.11:g.66769562C>T
GRCh37.p13 chr 1	NC_000001.10:g.67235245C>A
GRCh37.p13 chr 1	NC_000001.10:g.67235245C>T

Gene: DYNLT5, dynein light chain Tctex-type family member 5 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DYNLT5 transcript	NM_152665.3:c.120-825C>A	N/A	Intron Variant
DYNLT5 transcript variant X1	XM_047448666.1:c.69-825C>A	N/A	Intron Variant
DYNLT5 transcript variant X2	XM_047448667.1:c.120-825C… XM_047448667.1:c.120-825C>A	N/A	Intron Variant
DYNLT5 transcript variant X3	XM_047448668.1:c.120-825C… XM_047448668.1:c.120-825C>A	N/A	Intron Variant
DYNLT5 transcript variant X4	XM_047448675.1:c.120-825C… XM_047448675.1:c.120-825C>A	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	T
GRCh38.p14 chr 1	NC_000001.11:g.66769562=	NC_000001.11:g.66769562C>A	NC_000001.11:g.66769562C>T
GRCh37.p13 chr 1	NC_000001.10:g.67235245=	NC_000001.10:g.67235245C>A	NC_000001.10:g.67235245C>T
TCTEX1D1 transcript	NM_152665.2:c.120-825=	NM_152665.2:c.120-825C>A	NM_152665.2:c.120-825C>T
DYNLT5 transcript	NM_152665.3:c.120-825=	NM_152665.3:c.120-825C>A	NM_152665.3:c.120-825C>T
TCTEX1D1 transcript variant X1	XM_005270595.1:c.90-825=	XM_005270595.1:c.90-825C>A	XM_005270595.1:c.90-825C>T
DYNLT5 transcript variant X1	XM_047448666.1:c.69-825=	XM_047448666.1:c.69-825C>A	XM_047448666.1:c.69-825C>T
DYNLT5 transcript variant X2	XM_047448667.1:c.120-825=	XM_047448667.1:c.120-825C>A	XM_047448667.1:c.120-825C>T
DYNLT5 transcript variant X3	XM_047448668.1:c.120-825=	XM_047448668.1:c.120-825C>A	XM_047448668.1:c.120-825C>T
DYNLT5 transcript variant X4	XM_047448675.1:c.120-825=	XM_047448675.1:c.120-825C>A	XM_047448675.1:c.120-825C>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#.

56 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SSAHASNP	ss20452160	Apr 05, 2004 (121)
2	ABI	ss41102025	Mar 15, 2006 (126)
3	HUMANGENOME_JCVI	ss99214725	Feb 06, 2009 (130)
4	BGI	ss102749257	Feb 23, 2009 (131)
5	1000GENOMES	ss108273906	Jan 23, 2009 (130)
6	ENSEMBL	ss131806940	Dec 01, 2009 (131)
7	BCM-HGSC-SUB	ss205443372	Jul 04, 2010 (132)
8	1000GENOMES	ss218430706	Jul 14, 2010 (132)
9	1000GENOMES	ss230568055	Jul 14, 2010 (132)
10	1000GENOMES	ss238256276	Jul 15, 2010 (132)
11	GMI	ss275859397	May 04, 2012 (137)
12	PJP	ss290528620	May 09, 2011 (134)
13	TISHKOFF	ss554206461	Apr 25, 2013 (138)
14	SSMP	ss648078986	Apr 25, 2013 (138)
15	EVA-GONL	ss975246311	Aug 21, 2014 (142)
16	1000GENOMES	ss1291219104	Aug 21, 2014 (142)
17	EVA_GENOME_DK	ss1574120237	Apr 01, 2015 (144)
18	EVA_UK10K_ALSPAC	ss1600348350	Apr 01, 2015 (144)
19	EVA_UK10K_TWINSUK	ss1643342383	Apr 01, 2015 (144)
20	HAMMER_LAB	ss1794494910	Sep 08, 2015 (146)
21	WEILL_CORNELL_DGM	ss1918454303	Feb 12, 2016 (147)
22	JJLAB	ss2019744490	Sep 14, 2016 (149)
23	USC_VALOUEV	ss2147760276	Dec 20, 2016 (150)
24	HUMAN_LONGEVITY	ss2163185284	Dec 20, 2016 (150)
25	SYSTEMSBIOZJU	ss2624385973	Nov 08, 2017 (151)
26	GRF	ss2697677847	Nov 08, 2017 (151)
27	GNOMAD	ss2756068711	Nov 08, 2017 (151)
28	SWEGEN	ss2986947689	Nov 08, 2017 (151)
29	BIOINF_KMB_FNS_UNIBA	ss3023634014	Nov 08, 2017 (151)
30	CSHL	ss3343492610	Nov 08, 2017 (151)
31	URBANLAB	ss3646681094	Oct 11, 2018 (152)
32	EGCUT_WGS	ss3655017706	Jul 12, 2019 (153)
33	EVA_DECODE	ss3686932715	Jul 12, 2019 (153)
34	ACPOP	ss3727118892	Jul 12, 2019 (153)
35	EVA	ss3746305920	Jul 12, 2019 (153)
36	KHV_HUMAN_GENOMES	ss3799312574	Jul 12, 2019 (153)
37	EVA	ss3826214386	Apr 25, 2020 (154)
38	EVA	ss3836494617	Apr 25, 2020 (154)
39	EVA	ss3841901160	Apr 25, 2020 (154)
40	SGDP_PRJ	ss3849018257	Apr 25, 2020 (154)
41	KRGDB	ss3894045626	Apr 25, 2020 (154)
42	KOGIC	ss3944672166	Apr 25, 2020 (154)
43	TOPMED	ss4452615006	Apr 25, 2021 (155)
44	TOMMO_GENOMICS	ss5144315842	Apr 25, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5242552425	Oct 17, 2022 (156)
46	EVA	ss5319249317	Oct 17, 2022 (156)
47	HUGCELL_USP	ss5443587435	Oct 17, 2022 (156)
48	EVA	ss5505879805	Oct 17, 2022 (156)
49	1000G_HIGH_COVERAGE	ss5514971579	Oct 17, 2022 (156)
50	SANFORD_IMAGENETICS	ss5625691544	Oct 17, 2022 (156)
51	TOMMO_GENOMICS	ss5669192532	Oct 17, 2022 (156)
52	YY_MCH	ss5800667832	Oct 17, 2022 (156)
53	EVA	ss5832069792	Oct 17, 2022 (156)
54	EVA	ss5848941539	Oct 17, 2022 (156)
55	EVA	ss5908588162	Oct 17, 2022 (156)
56	EVA	ss5937530298	Oct 17, 2022 (156)
57	1000Genomes	NC_000001.10 - 67235245	Oct 11, 2018 (152)
58	1000Genomes_30x	NC_000001.11 - 66769562	Oct 17, 2022 (156)
59	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 67235245	Oct 11, 2018 (152)
60	Genetic variation in the Estonian population	NC_000001.10 - 67235245	Oct 11, 2018 (152)
61	The Danish reference pan genome	NC_000001.10 - 67235245	Apr 25, 2020 (154)
62	gnomAD - Genomes	NC_000001.11 - 66769562	Apr 25, 2021 (155)
63	Genome of the Netherlands Release 5	NC_000001.10 - 67235245	Apr 25, 2020 (154)
64	HapMap	NC_000001.11 - 66769562	Apr 25, 2020 (154)
65	KOREAN population from KRGDB	NC_000001.10 - 67235245	Apr 25, 2020 (154)
66	Korean Genome Project	NC_000001.11 - 66769562	Apr 25, 2020 (154)
67	Northern Sweden	NC_000001.10 - 67235245	Jul 12, 2019 (153)
68	Qatari	NC_000001.10 - 67235245	Apr 25, 2020 (154)
69	SGDP_PRJ	NC_000001.10 - 67235245	Apr 25, 2020 (154)
70	Siberian	NC_000001.10 - 67235245	Apr 25, 2020 (154)
71	8.3KJPN	NC_000001.10 - 67235245	Apr 25, 2021 (155)
72	14KJPN	NC_000001.11 - 66769562	Oct 17, 2022 (156)
73	TopMed	NC_000001.11 - 66769562	Apr 25, 2021 (155)
74	UK 10K study - Twins	NC_000001.10 - 67235245	Oct 11, 2018 (152)
75	A Vietnamese Genetic Variation Database	NC_000001.10 - 67235245	Jul 12, 2019 (153)
76	ALFA	NC_000001.11 - 66769562	Apr 25, 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)
rs74225038	Dec 02, 2009 (131)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
4755878807	NC_000001.11:66769561:C:A	NC_000001.11:66769561:C:A	(self)
ss108273906, ss205443372, ss275859397, ss290528620	NC_000001.9:67007832:C:T	NC_000001.11:66769561:C:T	(self)
1949089, 1067994, 755954, 1535955, 455830, 1223020, 403757, 496233, 1035237, 276630, 2285149, 1067994, 223622, ss218430706, ss230568055, ss238256276, ss554206461, ss648078986, ss975246311, ss1291219104, ss1574120237, ss1600348350, ss1643342383, ss1794494910, ss1918454303, ss2019744490, ss2147760276, ss2624385973, ss2697677847, ss2756068711, ss2986947689, ss3343492610, ss3655017706, ss3727118892, ss3746305920, ss3826214386, ss3836494617, ss3849018257, ss3894045626, ss5144315842, ss5319249317, ss5505879805, ss5625691544, ss5832069792, ss5937530298	NC_000001.10:67235244:C:T	NC_000001.11:66769561:C:T	(self)
2497514, 13744281, 87722, 1050167, 3029636, 16221341, 4755878807, ss2163185284, ss3023634014, ss3646681094, ss3686932715, ss3799312574, ss3841901160, ss3944672166, ss4452615006, ss5242552425, ss5443587435, ss5514971579, ss5669192532, ss5800667832, ss5848941539, ss5908588162	NC_000001.11:66769561:C:T	NC_000001.11:66769561:C:T	(self)
ss20452160	NT_032977.6:28798313:C:T	NC_000001.11:66769561:C:T	(self)
ss41102025, ss99214725, ss102749257, ss131806940	NT_032977.9:37207162:C:T	NC_000001.11:66769561: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 rs12727390

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

rs12727390