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dbSNP Short Genetic Variations

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.

rs778594

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr5:140647719 (GRCh38.p13) 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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.371623 (98365/264690, TOPMED)
C=0.417443 (72393/173420, GnomAD_exome)
C=0.387017 (54153/139924, GnomAD) (+ 18 more)
C=0.40384 (16055/39756, ALFA)
C=0.48995 (19155/39096, ExAC)
C=0.49481 (8293/16760, 8.3KJPN)
C=0.3776 (1891/5008, 1000G)
C=0.4522 (2026/4480, Estonian)
C=0.4183 (1612/3854, ALSPAC)
C=0.4159 (1542/3708, TWINSUK)
C=0.4180 (1223/2926, KOREAN)
C=0.4334 (794/1832, Korea1K)
C=0.3535 (632/1788, HapMap)
C=0.407 (406/998, GoNL)
C=0.448 (269/600, NorthernSweden)
C=0.378 (202/534, MGP)
T=0.323 (122/378, SGDP_PRJ)
C=0.301 (65/216, Qatari)
C=0.467 (99/212, Vietnamese)
C=0.20 (8/40, GENOME_DK)
T=0.37 (14/38, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
IK : 2KB Upstream Variant
MIR3655 : 2KB Upstream Variant
NDUFA2 : 2KB Upstream Variant (+ 1 more)
TMCO6 : 500B Downstream Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 5 NC_000005.10:g.140647719T>C
GRCh37.p13 chr 5 NC_000005.9:g.140027304T>C
NDUFA2 RefSeqGene NG_021417.1:g.5067A>G
Gene: NDUFA2, NADH:ubiquinone oxidoreductase subunit A2 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
NDUFA2 transcript variant 2 NM_001185012.2:c. N/A Upstream Transcript Variant
NDUFA2 transcript variant 1 NM_002488.5:c. N/A Upstream Transcript Variant
NDUFA2 transcript variant 3 NR_033697.2:n. N/A Upstream Transcript Variant
Gene: TMCO6, transmembrane and coiled-coil domains 6 (plus strand) : 500B Downstream Variant
Molecule type Change Amino acid[Codon] SO Term
TMCO6 transcript variant 1 NM_001300980.2:c. N/A N/A
TMCO6 transcript variant 3 NM_001300982.2:c. N/A N/A
TMCO6 transcript variant 2 NM_018502.5:c. N/A N/A
TMCO6 transcript variant X4 XM_011537663.2:c. N/A Downstream Transcript Variant
TMCO6 transcript variant X1 XM_005268477.1:c. N/A N/A
TMCO6 transcript variant X7 XM_011537665.2:c. N/A N/A
TMCO6 transcript variant X8 XM_011537668.2:c. N/A N/A
TMCO6 transcript variant X2 XM_017009617.2:c. N/A N/A
TMCO6 transcript variant X3 XM_017009618.1:c. N/A N/A
TMCO6 transcript variant X6 XM_017009619.1:c. N/A N/A
TMCO6 transcript variant X10 XM_017009620.1:c. N/A N/A
TMCO6 transcript variant X5 XM_024446124.1:c. N/A N/A
TMCO6 transcript variant X9 XM_024446125.1:c. N/A N/A
TMCO6 transcript variant X11 XM_024446126.1:c. N/A N/A
Gene: IK, IK cytokine (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
IK transcript NM_006083.4:c. N/A Upstream Transcript Variant
IK transcript variant X1 XR_002956156.1:n. N/A Upstream Transcript Variant
Gene: MIR3655, microRNA 3655 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR3655 transcript NR_037428.1:n. N/A Upstream Transcript 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.

Allele: C (allele ID: 297438 )
ClinVar Accession Disease Names Clinical Significance
RCV000333463.2 Mitochondrial complex I deficiency, nuclear type 1 Benign

ALFA Allele Frequency (New)
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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 39756 T=0.59616 C=0.40384
European Sub 30030 T=0.57945 C=0.42055
African Sub 4840 T=0.6890 C=0.3110
African Others Sub 176 T=0.739 C=0.261
African American Sub 4664 T=0.6872 C=0.3128
Asian Sub 184 T=0.549 C=0.451
East Asian Sub 124 T=0.597 C=0.403
Other Asian Sub 60 T=0.45 C=0.55
Latin American 1 Sub 242 T=0.624 C=0.376
Latin American 2 Sub 1210 T=0.6438 C=0.3562
South Asian Sub 120 T=0.583 C=0.417
Other Sub 3130 T=0.5955 C=0.4045


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 T=0.628377 C=0.371623
gnomAD - Exomes Global Study-wide 173420 T=0.582557 C=0.417443
gnomAD - Exomes European Sub 87112 T=0.56268 C=0.43732
gnomAD - Exomes Asian Sub 37748 T=0.57765 C=0.42235
gnomAD - Exomes American Sub 25726 T=0.61568 C=0.38432
gnomAD - Exomes African Sub 9200 T=0.7111 C=0.2889
gnomAD - Exomes Ashkenazi Jewish Sub 8788 T=0.5756 C=0.4244
gnomAD - Exomes Other Sub 4846 T=0.5710 C=0.4290
gnomAD - Genomes Global Study-wide 139924 T=0.612983 C=0.387017
gnomAD - Genomes European Sub 75828 T=0.56788 C=0.43212
gnomAD - Genomes African Sub 41888 T=0.70650 C=0.29350
gnomAD - Genomes American Sub 13620 T=0.60485 C=0.39515
gnomAD - Genomes Ashkenazi Jewish Sub 3316 T=0.5654 C=0.4346
gnomAD - Genomes East Asian Sub 3122 T=0.5445 C=0.4555
gnomAD - Genomes Other Sub 2150 T=0.6060 C=0.3940
ExAC Global Study-wide 39096 T=0.51005 C=0.48995
ExAC Europe Sub 22482 T=0.47198 C=0.52802
ExAC Asian Sub 12160 T=0.55773 C=0.44227
ExAC African Sub 2712 T=0.6110 C=0.3890
ExAC American Sub 1386 T=0.5115 C=0.4885
ExAC Other Sub 356 T=0.511 C=0.489
8.3KJPN JAPANESE Study-wide 16760 T=0.50519 C=0.49481
1000Genomes Global Study-wide 5008 T=0.6224 C=0.3776
1000Genomes African Sub 1322 T=0.7269 C=0.2731
1000Genomes East Asian Sub 1008 T=0.5506 C=0.4494
1000Genomes Europe Sub 1006 T=0.5964 C=0.4036
1000Genomes South Asian Sub 978 T=0.551 C=0.449
1000Genomes American Sub 694 T=0.666 C=0.334
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.5478 C=0.4522
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.5817 C=0.4183
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.5841 C=0.4159
KOREAN population from KRGDB KOREAN Study-wide 2926 T=0.5820 C=0.4180
Korean Genome Project KOREAN Study-wide 1832 T=0.5666 C=0.4334
HapMap Global Study-wide 1788 T=0.6465 C=0.3535
HapMap African Sub 690 T=0.717 C=0.283
HapMap American Sub 670 T=0.596 C=0.404
HapMap Asian Sub 252 T=0.556 C=0.444
HapMap Europe Sub 176 T=0.693 C=0.307
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 T=0.593 C=0.407
Northern Sweden ACPOP Study-wide 600 T=0.552 C=0.448
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 T=0.622 C=0.378
SGDP_PRJ Global Study-wide 378 T=0.323 C=0.677
Qatari Global Study-wide 216 T=0.699 C=0.301
A Vietnamese Genetic Variation Database Global Study-wide 212 T=0.533 C=0.467
The Danish reference pan genome Danish Study-wide 40 T=0.80 C=0.20
Siberian Global Study-wide 38 T=0.37 C=0.63
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 T= C
GRCh38.p13 chr 5 NC_000005.10:g.140647719= NC_000005.10:g.140647719T>C
GRCh37.p13 chr 5 NC_000005.9:g.140027304= NC_000005.9:g.140027304T>C
NDUFA2 RefSeqGene NG_021417.1:g.5067= NG_021417.1:g.5067A>G
NDUFA2 transcript variant 1 NM_002488.4:c.-136= NM_002488.4:c.-136A>G
NDUFA2 transcript variant 3 NR_033697.1:n.67= NR_033697.1:n.67A>G
NDUFA2 transcript variant 2 NM_001185012.1:c.-136= NM_001185012.1:c.-136A>G
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#.

83 SubSNP, 21 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 KWOK ss910342 Oct 05, 2000 (86)
2 YUSUKE ss3215586 Sep 28, 2001 (100)
3 TSC-CSHL ss3289850 Sep 28, 2001 (100)
4 SC_JCM ss3607513 Sep 28, 2001 (100)
5 CGAP-GAI ss4323036 Jan 04, 2002 (102)
6 RIKENSNPRC ss5601033 Dec 12, 2002 (110)
7 KYUGEN ss28461091 Sep 20, 2004 (123)
8 KYUGEN ss28461092 Sep 20, 2004 (123)
9 ABI ss44609009 Mar 14, 2006 (126)
10 ILLUMINA ss65772961 Oct 13, 2006 (127)
11 ILLUMINA ss74898232 Dec 06, 2007 (129)
12 BCMHGSC_JDW ss93269064 Mar 24, 2008 (129)
13 1000GENOMES ss109460584 Jan 24, 2009 (130)
14 ILLUMINA-UK ss116832913 Feb 14, 2009 (130)
15 KRIBB_YJKIM ss119367757 Dec 01, 2009 (131)
16 ENSEMBL ss143483902 Dec 01, 2009 (131)
17 ILLUMINA ss152536450 Dec 01, 2009 (131)
18 ILLUMINA ss159102641 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss162714020 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss167145382 Jul 04, 2010 (132)
21 ILLUMINA ss168871025 Jul 04, 2010 (132)
22 ILLUMINA ss174547890 Jul 04, 2010 (132)
23 BUSHMAN ss200936900 Jul 04, 2010 (132)
24 BCM-HGSC-SUB ss206709378 Jul 04, 2010 (132)
25 1000GENOMES ss221997041 Jul 14, 2010 (132)
26 1000GENOMES ss233170977 Jul 14, 2010 (132)
27 1000GENOMES ss240287692 Jul 15, 2010 (132)
28 BL ss253846293 May 09, 2011 (134)
29 GMI ss278502538 May 04, 2012 (137)
30 PJP ss293471512 May 09, 2011 (134)
31 ILLUMINA ss532729395 Sep 08, 2015 (146)
32 TISHKOFF ss558749504 Apr 25, 2013 (138)
33 SSMP ss652649743 Apr 25, 2013 (138)
34 ILLUMINA ss832615437 Jul 13, 2019 (153)
35 EVA-GONL ss982186018 Aug 21, 2014 (142)
36 JMKIDD_LAB ss1073085609 Aug 21, 2014 (142)
37 1000GENOMES ss1317463766 Aug 21, 2014 (142)
38 EVA_GENOME_DK ss1581373582 Apr 01, 2015 (144)
39 EVA_DECODE ss1591715442 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1614144161 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1657138194 Apr 01, 2015 (144)
42 EVA_EXAC ss1687976856 Apr 01, 2015 (144)
43 EVA_MGP ss1711099243 Apr 01, 2015 (144)
44 EVA_SVP ss1712804461 Apr 01, 2015 (144)
45 HAMMER_LAB ss1804107050 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1925441260 Feb 12, 2016 (147)
47 GENOMED ss1970220903 Jul 19, 2016 (147)
48 JJLAB ss2023326068 Sep 14, 2016 (149)
49 USC_VALOUEV ss2151484454 Dec 20, 2016 (150)
50 HUMAN_LONGEVITY ss2278679680 Dec 20, 2016 (150)
51 TOPMED ss2446990582 Dec 20, 2016 (150)
52 SYSTEMSBIOZJU ss2626150843 Nov 08, 2017 (151)
53 GRF ss2707049728 Nov 08, 2017 (151)
54 GNOMAD ss2735265036 Nov 08, 2017 (151)
55 GNOMAD ss2747462755 Nov 08, 2017 (151)
56 GNOMAD ss2831495520 Nov 08, 2017 (151)
57 SWEGEN ss2997891341 Nov 08, 2017 (151)
58 CSHL ss3346653645 Nov 08, 2017 (151)
59 TOPMED ss3480330377 Nov 08, 2017 (151)
60 ILLUMINA ss3629353861 Oct 12, 2018 (152)
61 ILLUMINA ss3638583906 Oct 12, 2018 (152)
62 ILLUMINA ss3638583907 Oct 12, 2018 (152)
63 ILLUMINA ss3643527642 Oct 12, 2018 (152)
64 OMUKHERJEE_ADBS ss3646325026 Oct 12, 2018 (152)
65 EGCUT_WGS ss3665807475 Jul 13, 2019 (153)
66 EVA_DECODE ss3715819915 Jul 13, 2019 (153)
67 ACPOP ss3732867906 Jul 13, 2019 (153)
68 EVA ss3764136238 Jul 13, 2019 (153)
69 KHV_HUMAN_GENOMES ss3807306460 Jul 13, 2019 (153)
70 EVA ss3825681208 Apr 26, 2020 (154)
71 EVA ss3829533075 Apr 26, 2020 (154)
72 EVA ss3838241110 Apr 26, 2020 (154)
73 EVA ss3843683909 Apr 26, 2020 (154)
74 SGDP_PRJ ss3863101163 Apr 26, 2020 (154)
75 KRGDB ss3909761694 Apr 26, 2020 (154)
76 KOGIC ss3957765121 Apr 26, 2020 (154)
77 FSA-LAB ss3984317259 Apr 26, 2021 (155)
78 FSA-LAB ss3984317260 Apr 26, 2021 (155)
79 EVA ss3986031640 Apr 26, 2021 (155)
80 EVA ss3986320852 Apr 26, 2021 (155)
81 TOPMED ss4680915108 Apr 26, 2021 (155)
82 TOMMO_GENOMICS ss5174424920 Apr 26, 2021 (155)
83 EVA ss5237187282 Apr 26, 2021 (155)
84 1000Genomes NC_000005.9 - 140027304 Oct 12, 2018 (152)
85 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 140027304 Oct 12, 2018 (152)
86 Genetic variation in the Estonian population NC_000005.9 - 140027304 Oct 12, 2018 (152)
87 ExAC NC_000005.9 - 140027304 Oct 12, 2018 (152)
88 The Danish reference pan genome NC_000005.9 - 140027304 Apr 26, 2020 (154)
89 gnomAD - Genomes NC_000005.10 - 140647719 Apr 26, 2021 (155)
90 gnomAD - Exomes NC_000005.9 - 140027304 Jul 13, 2019 (153)
91 Genome of the Netherlands Release 5 NC_000005.9 - 140027304 Apr 26, 2020 (154)
92 HapMap NC_000005.10 - 140647719 Apr 26, 2020 (154)
93 KOREAN population from KRGDB NC_000005.9 - 140027304 Apr 26, 2020 (154)
94 Korean Genome Project NC_000005.10 - 140647719 Apr 26, 2020 (154)
95 Medical Genome Project healthy controls from Spanish population NC_000005.9 - 140027304 Apr 26, 2020 (154)
96 Northern Sweden NC_000005.9 - 140027304 Jul 13, 2019 (153)
97 Qatari NC_000005.9 - 140027304 Apr 26, 2020 (154)
98 SGDP_PRJ NC_000005.9 - 140027304 Apr 26, 2020 (154)
99 Siberian NC_000005.9 - 140027304 Apr 26, 2020 (154)
100 8.3KJPN NC_000005.9 - 140027304 Apr 26, 2021 (155)
101 TopMed NC_000005.10 - 140647719 Apr 26, 2021 (155)
102 UK 10K study - Twins NC_000005.9 - 140027304 Oct 12, 2018 (152)
103 A Vietnamese Genetic Variation Database NC_000005.9 - 140027304 Jul 13, 2019 (153)
104 ALFA NC_000005.10 - 140647719 Apr 26, 2021 (155)
105 ClinVar RCV000333463.2 Apr 26, 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)
rs11547210 Oct 08, 2004 (123)
rs386420625 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss93269064, ss109460584, ss116832913, ss162714020, ss167145382, ss200936900, ss206709378, ss253846293, ss278502538, ss293471512, ss1591715442, ss1712804461, ss3643527642 NC_000005.8:140007487:T:C NC_000005.10:140647718:T:C (self)
29151066, 16216451, 11545723, 7982412, 7538521, 4389512, 7203229, 16939088, 215003, 6152771, 7483190, 15118143, 4000808, 32394227, 16216451, 3593855, ss221997041, ss233170977, ss240287692, ss532729395, ss558749504, ss652649743, ss832615437, ss982186018, ss1073085609, ss1317463766, ss1581373582, ss1614144161, ss1657138194, ss1687976856, ss1711099243, ss1804107050, ss1925441260, ss1970220903, ss2023326068, ss2151484454, ss2446990582, ss2626150843, ss2707049728, ss2735265036, ss2747462755, ss2831495520, ss2997891341, ss3346653645, ss3629353861, ss3638583906, ss3638583907, ss3646325026, ss3665807475, ss3732867906, ss3764136238, ss3825681208, ss3829533075, ss3838241110, ss3863101163, ss3909761694, ss3984317259, ss3984317260, ss3986031640, ss3986320852, ss5174424920 NC_000005.9:140027303:T:C NC_000005.10:140647718:T:C (self)
RCV000333463.2, 206223101, 2979748, 14143122, 324094879, 518292665, 4111209554, ss2278679680, ss3480330377, ss3715819915, ss3807306460, ss3843683909, ss3957765121, ss4680915108, ss5237187282 NC_000005.10:140647718:T:C NC_000005.10:140647718:T:C (self)
ss910342, ss3215586, ss3289850, ss3607513, ss4323036, ss5601033, ss28461091, ss28461092, ss44609009, ss65772961, ss74898232, ss119367757, ss143483902, ss152536450, ss159102641, ss168871025, ss174547890 NT_029289.11:1190230:T:C NC_000005.10:140647718:T:C (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 rs778594

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.post596+ae089ad