Skip to main page content
Accesskeys

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 Aliases 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.

rs4820889

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr22:30623057 (GRCh38.p12) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.05126 (6436/125568, TOPMED)
A=0.03511 (4262/121386, ExAC)
A=0.0596 (4689/78692, PAGE_STUDY) (+ 5 more)
A=0.0493 (1537/31200, GnomAD)
A=0.0532 (692/13006, GO-ESP)
A=0.057 (283/5008, 1000G)
A=0.032 (145/4480, Estonian)
A=0.03 (17/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
TCN2 : Missense Variant
Publications
3 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.p12 chr 22 NC_000022.11:g.30623057G>A
GRCh38.p12 chr 22 NC_000022.11:g.30623057G>C
GRCh37.p13 chr 22 NC_000022.10:g.31019044G>A
GRCh37.p13 chr 22 NC_000022.10:g.31019044G>C
TCN2 RefSeqGene (LRG_116) NG_007263.1:g.20884G>A
TCN2 RefSeqGene (LRG_116) NG_007263.1:g.20884G>C
Gene: TCN2, transcobalamin 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TCN2 transcript variant 2 NM_001184726.1:c.1115G>A R [CGA] > Q [CAA] Coding Sequence Variant
transcobalamin-2 isoform 2 precursor NP_001171655.1:p.Arg372Gln R (Arg) > Q (Gln) Missense Variant
TCN2 transcript variant 2 NM_001184726.1:c.1115G>C R [CGA] > P [CCA] Coding Sequence Variant
transcobalamin-2 isoform 2 precursor NP_001171655.1:p.Arg372Pro R (Arg) > P (Pro) Missense Variant
TCN2 transcript variant 1 NM_000355.4:c.1196G>A R [CGA] > Q [CAA] Coding Sequence Variant
transcobalamin-2 isoform 1 precursor NP_000346.2:p.Arg399Gln R (Arg) > Q (Gln) Missense Variant
TCN2 transcript variant 1 NM_000355.4:c.1196G>C R [CGA] > P [CCA] Coding Sequence Variant
transcobalamin-2 isoform 1 precursor NP_000346.2:p.Arg399Pro R (Arg) > P (Pro) Missense 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: A (allele ID: 347421 )
ClinVar Accession Disease Names Clinical Significance
RCV000353236.2 Transcobalamin II deficiency Benign-Likely-Benign
RCV000506035.2 not specified Benign
RCV000755401.1 not provided Benign
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 125568 G=0.94874 A=0.05126
ExAC Global Study-wide 121386 G=0.96489 A=0.03511
ExAC Europe Sub 73340 G=0.9715 A=0.0285
ExAC Asian Sub 25160 G=0.9704 A=0.0296
ExAC American Sub 11572 G=0.9799 A=0.0201
ExAC African Sub 10406 G=0.8879 A=0.1121
ExAC Other Sub 908 G=0.97 A=0.03
The PAGE Study Global Study-wide 78692 G=0.9404 A=0.0596
The PAGE Study AfricanAmerican Sub 32514 G=0.8980 A=0.1020
The PAGE Study Mexican Sub 10808 G=0.9782 A=0.0218
The PAGE Study Asian Sub 8316 G=0.997 A=0.003
The PAGE Study PuertoRican Sub 7916 G=0.950 A=0.050
The PAGE Study NativeHawaiian Sub 4534 G=0.986 A=0.014
The PAGE Study Cuban Sub 4230 G=0.958 A=0.042
The PAGE Study Dominican Sub 3828 G=0.931 A=0.069
The PAGE Study CentralAmerican Sub 2450 G=0.968 A=0.032
The PAGE Study SouthAmerican Sub 1980 G=0.979 A=0.021
The PAGE Study NativeAmerican Sub 1260 G=0.960 A=0.040
The PAGE Study SouthAsian Sub 856 G=0.96 A=0.04
gnomAD - Genomes Global Study-wide 31200 G=0.9507 A=0.0493
gnomAD - Genomes European Sub 18778 G=0.9726 A=0.0274
gnomAD - Genomes African Sub 8650 G=0.891 A=0.109
gnomAD - Genomes East Asian Sub 1556 G=0.997 A=0.003
gnomAD - Genomes Other Sub 1080 G=0.966 A=0.034
gnomAD - Genomes American Sub 848 G=0.97 A=0.03
gnomAD - Genomes Ashkenazi Jewish Sub 288 G=0.97 A=0.03
GO Exome Sequencing Project Global Study-wide 13006 G=0.9468 A=0.0532
GO Exome Sequencing Project European American Sub 8600 G=0.970 A=0.030
GO Exome Sequencing Project African American Sub 4406 G=0.901 A=0.099
1000Genomes Global Study-wide 5008 G=0.943 A=0.057
1000Genomes African Sub 1322 G=0.859 A=0.141
1000Genomes East Asian Sub 1008 G=0.999 A=0.001
1000Genomes Europe Sub 1006 G=0.971 A=0.029
1000Genomes South Asian Sub 978 G=0.95 A=0.05
1000Genomes American Sub 694 G=0.97 A=0.03
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.968 A=0.032
Northern Sweden ACPOP Study-wide 600 G=0.97 A=0.03
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 C Note
GRCh38.p12 chr 22 NC_000022.11:g.30...

NC_000022.11:g.30623057=

NC_000022.11:g.30...

NC_000022.11:g.30623057G>A

NC_000022.11:g.30...

NC_000022.11:g.30623057G>C

GRCh37.p13 chr 22 NC_000022.10:g.31...

NC_000022.10:g.31019044=

NC_000022.10:g.31...

NC_000022.10:g.31019044G>A

NC_000022.10:g.31...

NC_000022.10:g.31019044G>C

TCN2 RefSeqGene (LRG_116) NG_007263.1:g.20884= NG_007263.1:g.208...

NG_007263.1:g.20884G>A

NG_007263.1:g.208...

NG_007263.1:g.20884G>C

TCN2 transcript variant 1 NM_000355.4:c.1196= NM_000355.4:c.119...

NM_000355.4:c.1196G>A

NM_000355.4:c.119...

NM_000355.4:c.1196G>C

TCN2 transcript variant 1 NM_000355.3:c.1196= NM_000355.3:c.119...

NM_000355.3:c.1196G>A

NM_000355.3:c.119...

NM_000355.3:c.1196G>C

TCN2 transcript variant 2 NM_001184726.1:c....

NM_001184726.1:c.1115=

NM_001184726.1:c....

NM_001184726.1:c.1115G>A

NM_001184726.1:c....

NM_001184726.1:c.1115G>C

transcobalamin-2 isoform 1 precursor NP_000346.2:p.Arg...

NP_000346.2:p.Arg399=

NP_000346.2:p.Arg...

NP_000346.2:p.Arg399Gln

NP_000346.2:p.Arg...

NP_000346.2:p.Arg399Pro

transcobalamin-2 isoform 2 precursor NP_001171655.1:p....

NP_001171655.1:p.Arg372=

NP_001171655.1:p....

NP_001171655.1:p.Arg372Gln

NP_001171655.1:p....

NP_001171655.1:p.Arg372Pro

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#.

99 SubSNP, 14 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6657226 Feb 20, 2003 (111)
2 SC_SNP ss8292570 Apr 21, 2003 (114)
3 ILLUMINA ss66684890 Dec 02, 2006 (127)
4 ILLUMINA ss67382466 Dec 02, 2006 (127)
5 ILLUMINA ss67759946 Dec 02, 2006 (127)
6 PERLEGEN ss69274476 May 18, 2007 (127)
7 ILLUMINA ss70827893 May 26, 2008 (130)
8 ILLUMINA ss71410197 May 18, 2007 (127)
9 SI_EXO ss71646219 May 18, 2007 (127)
10 AFFY ss74807679 Aug 16, 2007 (128)
11 ILLUMINA ss75563450 Dec 06, 2007 (129)
12 AFFY ss76658775 Dec 06, 2007 (129)
13 ILLUMINA ss79197212 Dec 15, 2007 (130)
14 KRIBB_YJKIM ss84365137 Dec 15, 2007 (130)
15 CORNELL ss86264988 Mar 23, 2008 (129)
16 ILLUMINA ss122399381 Dec 01, 2009 (131)
17 ILLUMINA ss154320386 Dec 01, 2009 (131)
18 ILLUMINA ss159497043 Dec 01, 2009 (131)
19 SEATTLESEQ ss159744231 Dec 01, 2009 (131)
20 ILLUMINA ss160716184 Dec 01, 2009 (131)
21 ILLUMINA ss171933269 Jul 04, 2010 (132)
22 ILLUMINA ss173829563 Jul 04, 2010 (132)
23 BUSHMAN ss204074455 Jul 04, 2010 (132)
24 1000GENOMES ss228657725 Jul 14, 2010 (132)
25 1000GENOMES ss238052046 Jul 15, 2010 (132)
26 NHLBI-ESP ss342540360 May 09, 2011 (134)
27 ILLUMINA ss481062264 May 04, 2012 (137)
28 ILLUMINA ss481084040 May 04, 2012 (137)
29 ILLUMINA ss482078561 Sep 08, 2015 (146)
30 ILLUMINA ss485326181 May 04, 2012 (137)
31 1000GENOMES ss491191003 May 04, 2012 (137)
32 EXOME_CHIP ss491570367 May 04, 2012 (137)
33 CLINSEQ_SNP ss491822857 May 04, 2012 (137)
34 ILLUMINA ss537279267 Sep 08, 2015 (146)
35 TISHKOFF ss566610643 Apr 25, 2013 (138)
36 SSMP ss662542003 Apr 25, 2013 (138)
37 ILLUMINA ss778920800 Sep 08, 2015 (146)
38 ILLUMINA ss783108898 Sep 08, 2015 (146)
39 ILLUMINA ss784065939 Sep 08, 2015 (146)
40 ILLUMINA ss825527730 Apr 01, 2015 (144)
41 ILLUMINA ss832367549 Sep 08, 2015 (146)
42 ILLUMINA ss833008418 Jul 13, 2019 (153)
43 ILLUMINA ss834382230 Sep 08, 2015 (146)
44 JMKIDD_LAB ss974512547 Aug 21, 2014 (142)
45 EVA-GONL ss995306015 Aug 21, 2014 (142)
46 JMKIDD_LAB ss1067605491 Aug 21, 2014 (142)
47 JMKIDD_LAB ss1082626388 Aug 21, 2014 (142)
48 1000GENOMES ss1366999679 Aug 21, 2014 (142)
49 DDI ss1429244030 Apr 01, 2015 (144)
50 EVA_GENOME_DK ss1579734928 Apr 01, 2015 (144)
51 EVA_FINRISK ss1584127347 Apr 01, 2015 (144)
52 EVA_UK10K_ALSPAC ss1639905547 Apr 01, 2015 (144)
53 EVA_UK10K_ALSPAC ss1639905548 Apr 01, 2015 (144)
54 EVA_UK10K_TWINSUK ss1682899580 Apr 01, 2015 (144)
55 EVA_UK10K_TWINSUK ss1682899581 Apr 01, 2015 (144)
56 EVA_EXAC ss1694304375 Apr 01, 2015 (144)
57 EVA_DECODE ss1699375550 Apr 01, 2015 (144)
58 EVA_MGP ss1711566578 Apr 01, 2015 (144)
59 EVA_SVP ss1713737678 Apr 01, 2015 (144)
60 ILLUMINA ss1752418411 Sep 08, 2015 (146)
61 HAMMER_LAB ss1809769440 Sep 08, 2015 (146)
62 WEILL_CORNELL_DGM ss1938872399 Feb 12, 2016 (147)
63 ILLUMINA ss1959974896 Feb 12, 2016 (147)
64 JJLAB ss2030207809 Sep 14, 2016 (149)
65 USC_VALOUEV ss2158824389 Dec 20, 2016 (150)
66 HUMAN_LONGEVITY ss2246995465 Dec 20, 2016 (150)
67 TOPMED ss2413938643 Dec 20, 2016 (150)
68 ILLUMINA ss2633872417 Nov 08, 2017 (151)
69 GNOMAD ss2745076102 Nov 08, 2017 (151)
70 GNOMAD ss2750536119 Nov 08, 2017 (151)
71 GNOMAD ss2973917133 Nov 08, 2017 (151)
72 AFFY ss2985236952 Nov 08, 2017 (151)
73 SWEGEN ss3019233738 Nov 08, 2017 (151)
74 ILLUMINA ss3022181455 Nov 08, 2017 (151)
75 TOPMED ss3376108150 Nov 08, 2017 (151)
76 ILLUMINA ss3628523909 Oct 12, 2018 (152)
77 ILLUMINA ss3631824024 Oct 12, 2018 (152)
78 ILLUMINA ss3633271684 Oct 12, 2018 (152)
79 ILLUMINA ss3633987369 Oct 12, 2018 (152)
80 ILLUMINA ss3634865444 Oct 12, 2018 (152)
81 ILLUMINA ss3635671844 Oct 12, 2018 (152)
82 ILLUMINA ss3636561256 Oct 12, 2018 (152)
83 ILLUMINA ss3637424080 Oct 12, 2018 (152)
84 ILLUMINA ss3638379916 Oct 12, 2018 (152)
85 ILLUMINA ss3639193645 Oct 12, 2018 (152)
86 ILLUMINA ss3639613297 Oct 12, 2018 (152)
87 ILLUMINA ss3640572748 Oct 12, 2018 (152)
88 ILLUMINA ss3643339882 Oct 12, 2018 (152)
89 ILLUMINA ss3652644612 Oct 12, 2018 (152)
90 ILLUMINA ss3654004896 Oct 12, 2018 (152)
91 EGCUT_WGS ss3685730822 Jul 13, 2019 (153)
92 EVA_DECODE ss3708114016 Jul 13, 2019 (153)
93 ILLUMINA ss3725964550 Jul 13, 2019 (153)
94 ACPOP ss3743895135 Jul 13, 2019 (153)
95 ILLUMINA ss3745165300 Jul 13, 2019 (153)
96 EVA ss3759330090 Jul 13, 2019 (153)
97 PAGE_CC ss3772088115 Jul 13, 2019 (153)
98 ILLUMINA ss3772661221 Jul 13, 2019 (153)
99 KHV_HUMAN_GENOMES ss3822494461 Jul 13, 2019 (153)
100 1000Genomes NC_000022.10 - 31019044 Oct 12, 2018 (152)
101 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 44550382 (NC_000022.10:31019043:G:G 3747/3854, NC_000022.10:31019043:G:A 107/3854)
Row 44550383 (NC_000022.10:31019043:G:G 3853/3854, NC_000022.10:31019043:G:C 1/3854)

- Oct 12, 2018 (152)
102 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 44550382 (NC_000022.10:31019043:G:G 3747/3854, NC_000022.10:31019043:G:A 107/3854)
Row 44550383 (NC_000022.10:31019043:G:G 3853/3854, NC_000022.10:31019043:G:C 1/3854)

- Oct 12, 2018 (152)
103 Genetic variation in the Estonian population NC_000022.10 - 31019044 Oct 12, 2018 (152)
104 ExAC NC_000022.10 - 31019044 Oct 12, 2018 (152)
105 gnomAD - Genomes NC_000022.10 - 31019044 Jul 13, 2019 (153)
106 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 14406208 (NC_000022.10:31019043:G:G 243412/251458, NC_000022.10:31019043:G:A 8046/251458)
Row 14406209 (NC_000022.10:31019043:G:G 251457/251458, NC_000022.10:31019043:G:C 1/251458)

- Jul 13, 2019 (153)
107 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 14406208 (NC_000022.10:31019043:G:G 243412/251458, NC_000022.10:31019043:G:A 8046/251458)
Row 14406209 (NC_000022.10:31019043:G:G 251457/251458, NC_000022.10:31019043:G:C 1/251458)

- Jul 13, 2019 (153)
108 GO Exome Sequencing Project NC_000022.10 - 31019044 Oct 12, 2018 (152)
109 Northern Sweden NC_000022.10 - 31019044 Jul 13, 2019 (153)
110 The PAGE Study NC_000022.11 - 30623057 Jul 13, 2019 (153)
111 TopMed NC_000022.11 - 30623057 Oct 12, 2018 (152)
112 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 44550382 (NC_000022.10:31019043:G:G 3610/3708, NC_000022.10:31019043:G:A 98/3708)
Row 44550383 (NC_000022.10:31019043:G:G 3708/3708, NC_000022.10:31019043:G:C 0/3708)

- Oct 12, 2018 (152)
113 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 44550382 (NC_000022.10:31019043:G:G 3610/3708, NC_000022.10:31019043:G:A 98/3708)
Row 44550383 (NC_000022.10:31019043:G:G 3708/3708, NC_000022.10:31019043:G:C 0/3708)

- Oct 12, 2018 (152)
114 ClinVar RCV000353236.2 Oct 12, 2018 (152)
115 ClinVar RCV000506035.2 Jul 13, 2019 (153)
116 ClinVar RCV000755401.1 Jul 13, 2019 (153)
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)
rs52835526 Sep 21, 2007 (128)
rs60986198 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss3639193645, ss3639613297 NC_000022.8:29343597:G:A NC_000022.11:30623056:G:A (self)
ss76658775, ss204074455, ss481062264, ss491822857, ss825527730, ss1699375550, ss1713737678, ss3643339882 NC_000022.9:29349043:G:A NC_000022.11:30623056:G:A (self)
80545513, 31469070, 5882317, 219701874, 1895379, 17180000, ss228657725, ss238052046, ss342540360, ss481084040, ss482078561, ss485326181, ss491191003, ss491570367, ss537279267, ss566610643, ss662542003, ss778920800, ss783108898, ss784065939, ss832367549, ss833008418, ss834382230, ss974512547, ss995306015, ss1067605491, ss1082626388, ss1366999679, ss1429244030, ss1579734928, ss1584127347, ss1639905547, ss1682899580, ss1694304375, ss1711566578, ss1752418411, ss1809769440, ss1938872399, ss1959974896, ss2030207809, ss2158824389, ss2413938643, ss2633872417, ss2745076102, ss2750536119, ss2973917133, ss2985236952, ss3019233738, ss3022181455, ss3628523909, ss3631824024, ss3633271684, ss3633987369, ss3634865444, ss3635671844, ss3636561256, ss3637424080, ss3638379916, ss3640572748, ss3652644612, ss3654004896, ss3685730822, ss3743895135, ss3745165300, ss3759330090, ss3772661221 NC_000022.10:31019043:G:A NC_000022.11:30623056:G:A (self)
RCV000353236.2, RCV000506035.2, RCV000755401.1, 1309584, 239146870, ss2246995465, ss3376108150, ss3708114016, ss3725964550, ss3772088115, ss3822494461 NC_000022.11:30623056:G:A NC_000022.11:30623056:G:A (self)
ss6657226, ss8292570, ss66684890, ss67382466, ss67759946, ss69274476, ss70827893, ss71410197, ss71646219, ss74807679, ss75563450, ss79197212, ss84365137, ss86264988, ss122399381, ss154320386, ss159497043, ss159744231, ss160716184, ss171933269, ss173829563 NT_011520.12:10409612:G:A NC_000022.11:30623056:G:A (self)
ss1639905548, ss1682899581, ss2745076102 NC_000022.10:31019043:G:C NC_000022.11:30623056:G:C (self)
Help

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

3 citations for rs4820889
PMID Title Author Year Journal
21975197 Transcobalamin 2 variant associated with poststroke homocysteine modifies recurrent stroke risk. Hsu FC et al. 2011 Neurology
22188304 Polymorphisms in transcobalamin II gene is associated with coronary artery disease in Indian population. Garg G et al. 2012 Biomarkers
24048206 Neural tube defects, folic acid and methylation. Imbard A et al. 2013 International journal of environmental research and public health

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.post308+0fe9b3b