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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs10493419

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:66774094 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.100189 (26519/264690, TOPMED)
A=0.099661 (13949/139964, GnomAD)
A=0.11657 (6230/53444, ALFA) (+ 19 more)
A=0.14693 (4152/28258, 14KJPN)
A=0.14445 (2421/16760, 8.3KJPN)
A=0.1077 (690/6404, 1000G_30x)
A=0.1128 (565/5008, 1000G)
A=0.1094 (490/4480, Estonian)
A=0.1217 (469/3854, ALSPAC)
A=0.1335 (495/3708, TWINSUK)
A=0.1468 (430/2930, KOREAN)
A=0.0973 (184/1892, HapMap)
A=0.1392 (255/1832, Korea1K)
A=0.141 (141/998, GoNL)
A=0.078 (49/626, Chileans)
A=0.070 (42/600, NorthernSweden)
A=0.111 (24/216, Qatari)
A=0.207 (43/208, Vietnamese)
G=0.464 (52/112, SGDP_PRJ)
A=0.17 (7/40, GENOME_DK)
G=0.50 (8/16, Siberian)
A=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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 53444 G=0.88343 A=0.11657 0.781491 0.014632 0.203877 2
European Sub 35494 G=0.86682 A=0.13318 0.751845 0.0182 0.229954 0
African Sub 5616 G=0.9687 A=0.0313 0.938034 0.000712 0.061254 0
African Others Sub 192 G=0.990 A=0.010 0.979167 0.0 0.020833 0
African American Sub 5424 G=0.9679 A=0.0321 0.936578 0.000737 0.062684 0
Asian Sub 486 G=0.813 A=0.187 0.650206 0.024691 0.325103 1
East Asian Sub 388 G=0.802 A=0.198 0.634021 0.030928 0.335052 0
Other Asian Sub 98 G=0.86 A=0.14 0.714286 0.0 0.285714 1
Latin American 1 Sub 720 G=0.911 A=0.089 0.827778 0.005556 0.166667 0
Latin American 2 Sub 7062 G=0.9070 A=0.0930 0.821014 0.00708 0.171906 1
South Asian Sub 174 G=0.862 A=0.138 0.770115 0.045977 0.183908 3
Other Sub 3892 G=0.8738 A=0.1262 0.76259 0.014902 0.222508 0


Help

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=0.899811 A=0.100189
gnomAD - Genomes Global Study-wide 139964 G=0.900339 A=0.099661
gnomAD - Genomes European Sub 75794 G=0.86907 A=0.13093
gnomAD - Genomes African Sub 41964 G=0.96843 A=0.03157
gnomAD - Genomes American Sub 13616 G=0.89285 A=0.10715
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.8237 A=0.1763
gnomAD - Genomes East Asian Sub 3120 G=0.8647 A=0.1353
gnomAD - Genomes Other Sub 2146 G=0.8914 A=0.1086
Allele Frequency Aggregator Total Global 53444 G=0.88343 A=0.11657
Allele Frequency Aggregator European Sub 35494 G=0.86682 A=0.13318
Allele Frequency Aggregator Latin American 2 Sub 7062 G=0.9070 A=0.0930
Allele Frequency Aggregator African Sub 5616 G=0.9687 A=0.0313
Allele Frequency Aggregator Other Sub 3892 G=0.8738 A=0.1262
Allele Frequency Aggregator Latin American 1 Sub 720 G=0.911 A=0.089
Allele Frequency Aggregator Asian Sub 486 G=0.813 A=0.187
Allele Frequency Aggregator South Asian Sub 174 G=0.862 A=0.138
14KJPN JAPANESE Study-wide 28258 G=0.85307 A=0.14693
8.3KJPN JAPANESE Study-wide 16760 G=0.85555 A=0.14445
1000Genomes_30x Global Study-wide 6404 G=0.8923 A=0.1077
1000Genomes_30x African Sub 1786 G=0.9849 A=0.0151
1000Genomes_30x Europe Sub 1266 G=0.8515 A=0.1485
1000Genomes_30x South Asian Sub 1202 G=0.8195 A=0.1805
1000Genomes_30x East Asian Sub 1170 G=0.8487 A=0.1513
1000Genomes_30x American Sub 980 G=0.917 A=0.083
1000Genomes Global Study-wide 5008 G=0.8872 A=0.1128
1000Genomes African Sub 1322 G=0.9856 A=0.0144
1000Genomes East Asian Sub 1008 G=0.8512 A=0.1488
1000Genomes Europe Sub 1006 G=0.8489 A=0.1511
1000Genomes South Asian Sub 978 G=0.819 A=0.181
1000Genomes American Sub 694 G=0.903 A=0.097
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8906 A=0.1094
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8783 A=0.1217
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.8665 A=0.1335
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.8532 A=0.1468
HapMap Global Study-wide 1892 G=0.9027 A=0.0973
HapMap American Sub 770 G=0.865 A=0.135
HapMap African Sub 692 G=0.965 A=0.035
HapMap Asian Sub 254 G=0.870 A=0.130
HapMap Europe Sub 176 G=0.869 A=0.131
Korean Genome Project KOREAN Study-wide 1832 G=0.8608 A=0.1392
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.859 A=0.141
Chileans Chilean Study-wide 626 G=0.922 A=0.078
Northern Sweden ACPOP Study-wide 600 G=0.930 A=0.070
Qatari Global Study-wide 216 G=0.889 A=0.111
A Vietnamese Genetic Variation Database Global Study-wide 208 G=0.793 A=0.207
SGDP_PRJ Global Study-wide 112 G=0.464 A=0.536
The Danish reference pan genome Danish Study-wide 40 G=0.82 A=0.17
Siberian Global Study-wide 16 G=0.50 A=0.50
Help

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.66774094G>A
GRCh37.p13 chr 1 NC_000001.10:g.67239777G>A
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.212-2185G>A N/A Intron Variant
DYNLT5 transcript variant X1 XM_047448666.1:c.161-2185…

XM_047448666.1:c.161-2185G>A

 		N/A Intron Variant
DYNLT5 transcript variant X3 XM_047448668.1:c.*39+119G…

XM_047448668.1:c.*39+119G>A

 		N/A Intron Variant
DYNLT5 transcript variant X4 XM_047448675.1:c.*39+119G…

XM_047448675.1:c.*39+119G>A

 		N/A Intron Variant
DYNLT5 transcript variant X2 XM_047448667.1:c.*158= N/A 3 Prime UTR Variant
Help

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
Help

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
GRCh38.p14 chr 1 NC_000001.11:g.66774094= NC_000001.11:g.66774094G>A
GRCh37.p13 chr 1 NC_000001.10:g.67239777= NC_000001.10:g.67239777G>A
DYNLT5 transcript variant X2 XM_047448667.1:c.*158= XM_047448667.1:c.*158G>A
TCTEX1D1 transcript NM_152665.2:c.212-2185= NM_152665.2:c.212-2185G>A
DYNLT5 transcript NM_152665.3:c.212-2185= NM_152665.3:c.212-2185G>A
TCTEX1D1 transcript variant X1 XM_005270595.1:c.182-2185= XM_005270595.1:c.182-2185G>A
DYNLT5 transcript variant X1 XM_047448666.1:c.161-2185= XM_047448666.1:c.161-2185G>A
DYNLT5 transcript variant X3 XM_047448668.1:c.*39+119= XM_047448668.1:c.*39+119G>A
DYNLT5 transcript variant X4 XM_047448675.1:c.*39+119= XM_047448675.1:c.*39+119G>A
Help

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#.

67 SubSNP, 21 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss14882355 Dec 05, 2003 (119)
2 PERLEGEN ss24252910 Sep 20, 2004 (123)
3 ABI ss44026757 Mar 14, 2006 (126)
4 AFFY ss65979756 Dec 02, 2006 (127)
5 AFFY ss66415504 Dec 02, 2006 (127)
6 AFFY ss76176925 Dec 06, 2007 (129)
7 KRIBB_YJKIM ss82729410 Dec 16, 2007 (130)
8 HUMANGENOME_JCVI ss99214742 Feb 06, 2009 (130)
9 BGI ss102749274 Dec 01, 2009 (131)
10 1000GENOMES ss108273982 Jan 23, 2009 (130)
11 ENSEMBL ss138914502 Dec 01, 2009 (131)
12 ILLUMINA ss159901218 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss164466377 Jul 04, 2010 (132)
14 AFFY ss172719921 Jul 04, 2010 (132)
15 BCM-HGSC-SUB ss205182006 Jul 04, 2010 (132)
16 1000GENOMES ss230568077 Jul 14, 2010 (132)
17 1000GENOMES ss238256296 Jul 15, 2010 (132)
18 GMI ss275859417 May 04, 2012 (137)
19 PJP ss290528635 May 09, 2011 (134)
20 ILLUMINA ss479670836 Sep 08, 2015 (146)
21 SSMP ss648079094 Apr 25, 2013 (138)
22 EVA-GONL ss975246349 Aug 21, 2014 (142)
23 JMKIDD_LAB ss1067953385 Aug 21, 2014 (142)
24 1000GENOMES ss1291219231 Aug 21, 2014 (142)
25 DDI ss1425837214 Apr 01, 2015 (144)
26 EVA_GENOME_DK ss1574120293 Apr 01, 2015 (144)
27 EVA_DECODE ss1584615797 Apr 01, 2015 (144)
28 EVA_UK10K_ALSPAC ss1600348427 Apr 01, 2015 (144)
29 EVA_UK10K_TWINSUK ss1643342460 Apr 01, 2015 (144)
30 EVA_SVP ss1712340197 Apr 01, 2015 (144)
31 WEILL_CORNELL_DGM ss1918454348 Feb 12, 2016 (147)
32 JJLAB ss2019744515 Sep 14, 2016 (149)
33 USC_VALOUEV ss2147760297 Dec 20, 2016 (150)
34 HUMAN_LONGEVITY ss2163185546 Dec 20, 2016 (150)
35 SYSTEMSBIOZJU ss2624385993 Nov 08, 2017 (151)
36 GRF ss2697677875 Nov 08, 2017 (151)
37 GNOMAD ss2756069045 Nov 08, 2017 (151)
38 SWEGEN ss2986947743 Nov 08, 2017 (151)
39 BIOINF_KMB_FNS_UNIBA ss3023634033 Nov 08, 2017 (151)
40 CSHL ss3343492632 Nov 08, 2017 (151)
41 ILLUMINA ss3636005340 Oct 11, 2018 (152)
42 URBANLAB ss3646681114 Oct 11, 2018 (152)
43 EGCUT_WGS ss3655017762 Jul 12, 2019 (153)
44 EVA_DECODE ss3686932773 Jul 12, 2019 (153)
45 ACPOP ss3727118923 Jul 12, 2019 (153)
46 EVA ss3746305962 Jul 12, 2019 (153)
47 KHV_HUMAN_GENOMES ss3799312618 Jul 12, 2019 (153)
48 EVA ss3826214406 Apr 25, 2020 (154)
49 EVA ss3836494637 Apr 25, 2020 (154)
50 EVA ss3841901180 Apr 25, 2020 (154)
51 SGDP_PRJ ss3849018320 Apr 25, 2020 (154)
52 KRGDB ss3894045695 Apr 25, 2020 (154)
53 KOGIC ss3944672220 Apr 25, 2020 (154)
54 TOPMED ss4452616138 Apr 25, 2021 (155)
55 TOMMO_GENOMICS ss5144315963 Apr 25, 2021 (155)
56 1000G_HIGH_COVERAGE ss5242552533 Oct 17, 2022 (156)
57 EVA ss5319249519 Oct 17, 2022 (156)
58 HUGCELL_USP ss5443587537 Oct 17, 2022 (156)
59 EVA ss5505879827 Oct 17, 2022 (156)
60 1000G_HIGH_COVERAGE ss5514971735 Oct 17, 2022 (156)
61 SANFORD_IMAGENETICS ss5625691600 Oct 17, 2022 (156)
62 TOMMO_GENOMICS ss5669192692 Oct 17, 2022 (156)
63 YY_MCH ss5800667864 Oct 17, 2022 (156)
64 EVA ss5832069842 Oct 17, 2022 (156)
65 EVA ss5848941559 Oct 17, 2022 (156)
66 EVA ss5908588294 Oct 17, 2022 (156)
67 EVA ss5937530378 Oct 17, 2022 (156)
68 1000Genomes NC_000001.10 - 67239777 Oct 11, 2018 (152)
69 1000Genomes_30x NC_000001.11 - 66774094 Oct 17, 2022 (156)
70 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 67239777 Oct 11, 2018 (152)
71 Chileans NC_000001.10 - 67239777 Apr 25, 2020 (154)
72 Genetic variation in the Estonian population NC_000001.10 - 67239777 Oct 11, 2018 (152)
73 The Danish reference pan genome NC_000001.10 - 67239777 Apr 25, 2020 (154)
74 gnomAD - Genomes NC_000001.11 - 66774094 Apr 25, 2021 (155)
75 Genome of the Netherlands Release 5 NC_000001.10 - 67239777 Apr 25, 2020 (154)
76 HapMap NC_000001.11 - 66774094 Apr 25, 2020 (154)
77 KOREAN population from KRGDB NC_000001.10 - 67239777 Apr 25, 2020 (154)
78 Korean Genome Project NC_000001.11 - 66774094 Apr 25, 2020 (154)
79 Northern Sweden NC_000001.10 - 67239777 Jul 12, 2019 (153)
80 Qatari NC_000001.10 - 67239777 Apr 25, 2020 (154)
81 SGDP_PRJ NC_000001.10 - 67239777 Apr 25, 2020 (154)
82 Siberian NC_000001.10 - 67239777 Apr 25, 2020 (154)
83 8.3KJPN NC_000001.10 - 67239777 Apr 25, 2021 (155)
84 14KJPN NC_000001.11 - 66774094 Oct 17, 2022 (156)
85 TopMed NC_000001.11 - 66774094 Apr 25, 2021 (155)
86 UK 10K study - Twins NC_000001.10 - 67239777 Oct 11, 2018 (152)
87 A Vietnamese Genetic Variation Database NC_000001.10 - 67239777 Jul 12, 2019 (153)
88 ALFA NC_000001.11 - 66774094 Apr 25, 2021 (155)
Help

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)
rs17442100 Oct 07, 2004 (123)
rs61650297 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss108273982, ss164466377, ss205182006, ss275859417, ss290528635, ss1584615797, ss1712340197 NC_000001.9:67012364:G:A NC_000001.11:66774093:G:A (self)
1949219, 1068072, 10971, 756010, 1535976, 455868, 1223089, 403788, 496278, 1035300, 276651, 2285270, 1068072, 223648, ss230568077, ss238256296, ss479670836, ss648079094, ss975246349, ss1067953385, ss1291219231, ss1425837214, ss1574120293, ss1600348427, ss1643342460, ss1918454348, ss2019744515, ss2147760297, ss2624385993, ss2697677875, ss2756069045, ss2986947743, ss3343492632, ss3636005340, ss3655017762, ss3727118923, ss3746305962, ss3826214406, ss3836494637, ss3849018320, ss3894045695, ss5144315963, ss5319249519, ss5505879827, ss5625691600, ss5832069842, ss5937530378 NC_000001.10:67239776:G:A NC_000001.11:66774093:G:A (self)
2497670, 13745132, 87737, 1050221, 3029796, 16222473, 4756089783, ss2163185546, ss3023634033, ss3646681114, ss3686932773, ss3799312618, ss3841901180, ss3944672220, ss4452616138, ss5242552533, ss5443587537, ss5514971735, ss5669192692, ss5800667864, ss5848941559, ss5908588294 NC_000001.11:66774093:G:A NC_000001.11:66774093:G:A (self)
ss14882355, ss24252910, ss44026757, ss65979756, ss66415504, ss76176925, ss82729410, ss99214742, ss102749274, ss138914502, ss159901218, ss172719921 NT_032977.9:37211694:G:A NC_000001.11:66774093:G:A (self)
Help

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

No publications for rs10493419

Help

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.

Software version is: 2.0.1.post820+afb47a3d