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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.

rs55776826

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr19:1399057 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.138524 (36666/264690, TOPMED)
T=0.127797 (32021/250562, GnomAD_exome)
T=0.144108 (20191/140110, GnomAD) (+ 18 more)
T=0.129420 (15585/120422, ExAC)
T=0.14602 (4125/28250, ALFA)
T=0.01235 (207/16760, 8.3KJPN)
T=0.15293 (1989/13006, GO-ESP)
T=0.1132 (567/5008, 1000G)
T=0.1705 (764/4480, Estonian)
T=0.1492 (575/3854, ALSPAC)
T=0.1346 (499/3708, TWINSUK)
T=0.0116 (34/2920, KOREAN)
T=0.0142 (26/1832, Korea1K)
T=0.137 (137/998, GoNL)
T=0.088 (53/600, NorthernSweden)
T=0.112 (60/534, MGP)
T=0.102 (22/216, Qatari)
C=0.434 (53/122, SGDP_PRJ)
T=0.12 (5/40, GENOME_DK)
C=0.50 (6/12, Siberian)
T=0.50 (6/12, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
GAMT : Intron Variant
Publications
3 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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 28250 C=0.85398 T=0.14602
European Sub 20398 C=0.85219 T=0.14781
African Sub 3578 C=0.8457 T=0.1543
African Others Sub 122 C=0.836 T=0.164
African American Sub 3456 C=0.8461 T=0.1539
Asian Sub 172 C=0.977 T=0.023
East Asian Sub 114 C=0.982 T=0.018
Other Asian Sub 58 C=0.97 T=0.03
Latin American 1 Sub 154 C=0.838 T=0.162
Latin American 2 Sub 616 C=0.888 T=0.112
South Asian Sub 98 C=0.78 T=0.22
Other Sub 3234 C=0.8646 T=0.1354


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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.861476 T=0.138524
gnomAD - Exomes Global Study-wide 250562 C=0.872203 T=0.127797
gnomAD - Exomes European Sub 134690 C=0.858364 T=0.141636
gnomAD - Exomes Asian Sub 48998 C=0.90077 T=0.09923
gnomAD - Exomes American Sub 34566 C=0.89631 T=0.10369
gnomAD - Exomes African Sub 16162 C=0.83443 T=0.16557
gnomAD - Exomes Ashkenazi Jewish Sub 10022 C=0.89493 T=0.10507
gnomAD - Exomes Other Sub 6124 C=0.8744 T=0.1256
gnomAD - Genomes Global Study-wide 140110 C=0.855892 T=0.144108
gnomAD - Genomes European Sub 75874 C=0.85052 T=0.14948
gnomAD - Genomes African Sub 41986 C=0.84107 T=0.15893
gnomAD - Genomes American Sub 13642 C=0.89071 T=0.10929
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.8956 T=0.1044
gnomAD - Genomes East Asian Sub 3132 C=0.9872 T=0.0128
gnomAD - Genomes Other Sub 2152 C=0.8615 T=0.1385
ExAC Global Study-wide 120422 C=0.870580 T=0.129420
ExAC Europe Sub 72548 C=0.86335 T=0.13665
ExAC Asian Sub 25146 C=0.89553 T=0.10447
ExAC American Sub 11536 C=0.89658 T=0.10342
ExAC African Sub 10288 C=0.83019 T=0.16981
ExAC Other Sub 904 C=0.885 T=0.115
Allele Frequency Aggregator Total Global 28250 C=0.85398 T=0.14602
Allele Frequency Aggregator European Sub 20398 C=0.85219 T=0.14781
Allele Frequency Aggregator African Sub 3578 C=0.8457 T=0.1543
Allele Frequency Aggregator Other Sub 3234 C=0.8646 T=0.1354
Allele Frequency Aggregator Latin American 2 Sub 616 C=0.888 T=0.112
Allele Frequency Aggregator Asian Sub 172 C=0.977 T=0.023
Allele Frequency Aggregator Latin American 1 Sub 154 C=0.838 T=0.162
Allele Frequency Aggregator South Asian Sub 98 C=0.78 T=0.22
8.3KJPN JAPANESE Study-wide 16760 C=0.98765 T=0.01235
GO Exome Sequencing Project Global Study-wide 13006 C=0.84707 T=0.15293
GO Exome Sequencing Project European American Sub 8600 C=0.8562 T=0.1438
GO Exome Sequencing Project African American Sub 4406 C=0.8293 T=0.1707
1000Genomes Global Study-wide 5008 C=0.8868 T=0.1132
1000Genomes African Sub 1322 C=0.8328 T=0.1672
1000Genomes East Asian Sub 1008 C=0.9891 T=0.0109
1000Genomes Europe Sub 1006 C=0.8718 T=0.1282
1000Genomes South Asian Sub 978 C=0.855 T=0.145
1000Genomes American Sub 694 C=0.908 T=0.092
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.8295 T=0.1705
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.8508 T=0.1492
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.8654 T=0.1346
KOREAN population from KRGDB KOREAN Study-wide 2920 C=0.9884 T=0.0116
Korean Genome Project KOREAN Study-wide 1832 C=0.9858 T=0.0142
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.863 T=0.137
Northern Sweden ACPOP Study-wide 600 C=0.912 T=0.088
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.888 T=0.112
Qatari Global Study-wide 216 C=0.898 T=0.102
SGDP_PRJ Global Study-wide 122 C=0.434 T=0.566
The Danish reference pan genome Danish Study-wide 40 C=0.88 T=0.12
Siberian Global Study-wide 12 C=0.50 T=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.p13 chr 19 NC_000019.10:g.1399057C>T
GRCh37.p13 chr 19 NC_000019.9:g.1399056C>T
GAMT RefSeqGene NG_009785.1:g.7497G>A
Gene: GAMT, guanidinoacetate N-methyltransferase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GAMT transcript variant 1 NM_000156.6:c.460-31G>A N/A Intron Variant
GAMT transcript variant 2 NM_138924.3:c.460-31G>A N/A Intron 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: T (allele ID: 33919 )
ClinVar Accession Disease Names Clinical Significance
RCV000020143.3 Deficiency of guanidinoacetate methyltransferase Benign
RCV000829815.1 not provided Benign
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 C= T
GRCh38.p13 chr 19 NC_000019.10:g.1399057= NC_000019.10:g.1399057C>T
GRCh37.p13 chr 19 NC_000019.9:g.1399056= NC_000019.9:g.1399056C>T
GAMT RefSeqGene NG_009785.1:g.7497= NG_009785.1:g.7497G>A
GAMT transcript variant 1 NM_000156.5:c.460-31= NM_000156.5:c.460-31G>A
GAMT transcript variant 1 NM_000156.6:c.460-31= NM_000156.6:c.460-31G>A
GAMT transcript variant 2 NM_138924.2:c.460-31= NM_138924.2:c.460-31G>A
GAMT transcript variant 2 NM_138924.3:c.460-31= NM_138924.3:c.460-31G>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#.

56 SubSNP, 20 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 HGSV ss77276008 Dec 06, 2007 (129)
2 BCMHGSC_JDW ss90879953 Mar 24, 2008 (130)
3 1000GENOMES ss114735065 Jan 25, 2009 (130)
4 ENSEMBL ss137513171 Dec 01, 2009 (131)
5 COMPLETE_GENOMICS ss168856874 Jul 04, 2010 (132)
6 GENEREVIEWS ss179362391 Nov 18, 2009 (131)
7 BUSHMAN ss203582292 Jul 04, 2010 (132)
8 1000GENOMES ss210937416 Jul 14, 2010 (132)
9 1000GENOMES ss228006602 Jul 14, 2010 (132)
10 1000GENOMES ss237576925 Jul 15, 2010 (132)
11 PJP ss292172855 May 09, 2011 (134)
12 1000GENOMES ss491143739 May 04, 2012 (137)
13 ILLUMINA ss533099609 Sep 08, 2015 (146)
14 TISHKOFF ss565805750 Apr 25, 2013 (138)
15 SSMP ss661657849 Apr 25, 2013 (138)
16 NHLBI-ESP ss713457212 Apr 25, 2013 (138)
17 EVA-GONL ss994007984 Aug 21, 2014 (142)
18 JMKIDD_LAB ss1081709065 Aug 21, 2014 (142)
19 1000GENOMES ss1362047405 Aug 21, 2014 (142)
20 DDI ss1428310443 Apr 01, 2015 (144)
21 EVA_GENOME_DK ss1578524058 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1637424161 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1680418194 Apr 01, 2015 (144)
24 EVA_EXAC ss1693227220 Apr 01, 2015 (144)
25 EVA_DECODE ss1698070958 Apr 01, 2015 (144)
26 EVA_MGP ss1711491447 Apr 01, 2015 (144)
27 WEILL_CORNELL_DGM ss1937484803 Feb 12, 2016 (147)
28 JJLAB ss2029517818 Sep 14, 2016 (149)
29 USC_VALOUEV ss2158029465 Dec 20, 2016 (150)
30 HUMAN_LONGEVITY ss2223672969 Dec 20, 2016 (150)
31 TOPMED ss2389088499 Dec 20, 2016 (150)
32 GRF ss2702633200 Nov 08, 2017 (151)
33 GNOMAD ss2743414770 Nov 08, 2017 (151)
34 GNOMAD ss2749998640 Nov 08, 2017 (151)
35 GNOMAD ss2959554880 Nov 08, 2017 (151)
36 SWEGEN ss3016954379 Nov 08, 2017 (151)
37 BIOINF_KMB_FNS_UNIBA ss3028591498 Nov 08, 2017 (151)
38 TOPMED ss3285840722 Nov 08, 2017 (151)
39 CSHL ss3352158661 Nov 08, 2017 (151)
40 ILLUMINA ss3627870712 Oct 12, 2018 (152)
41 OMUKHERJEE_ADBS ss3646526251 Oct 12, 2018 (152)
42 EGCUT_WGS ss3683803782 Jul 13, 2019 (153)
43 EVA_DECODE ss3702177895 Jul 13, 2019 (153)
44 ACPOP ss3742783917 Jul 13, 2019 (153)
45 EVA ss3755718135 Jul 13, 2019 (153)
46 KHV_HUMAN_GENOMES ss3820972332 Jul 13, 2019 (153)
47 EVA ss3825209209 Apr 27, 2020 (154)
48 EVA ss3835308902 Apr 27, 2020 (154)
49 SGDP_PRJ ss3887584021 Apr 27, 2020 (154)
50 KRGDB ss3937509082 Apr 27, 2020 (154)
51 KOGIC ss3980639353 Apr 27, 2020 (154)
52 FSA-LAB ss3984137272 Apr 27, 2021 (155)
53 EVA ss3986765764 Apr 27, 2021 (155)
54 TOPMED ss5065471698 Apr 27, 2021 (155)
55 TOMMO_GENOMICS ss5226339480 Apr 27, 2021 (155)
56 EVA ss5237243937 Apr 27, 2021 (155)
57 1000Genomes NC_000019.9 - 1399056 Oct 12, 2018 (152)
58 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 1399056 Oct 12, 2018 (152)
59 Genetic variation in the Estonian population NC_000019.9 - 1399056 Oct 12, 2018 (152)
60 ExAC NC_000019.9 - 1399056 Oct 12, 2018 (152)
61 The Danish reference pan genome NC_000019.9 - 1399056 Apr 27, 2020 (154)
62 gnomAD - Genomes NC_000019.10 - 1399057 Apr 27, 2021 (155)
63 gnomAD - Exomes NC_000019.9 - 1399056 Jul 13, 2019 (153)
64 GO Exome Sequencing Project NC_000019.9 - 1399056 Oct 12, 2018 (152)
65 Genome of the Netherlands Release 5 NC_000019.9 - 1399056 Apr 27, 2020 (154)
66 KOREAN population from KRGDB NC_000019.9 - 1399056 Apr 27, 2020 (154)
67 Korean Genome Project NC_000019.10 - 1399057 Apr 27, 2020 (154)
68 Medical Genome Project healthy controls from Spanish population NC_000019.9 - 1399056 Apr 27, 2020 (154)
69 Northern Sweden NC_000019.9 - 1399056 Jul 13, 2019 (153)
70 Qatari NC_000019.9 - 1399056 Apr 27, 2020 (154)
71 SGDP_PRJ NC_000019.9 - 1399056 Apr 27, 2020 (154)
72 Siberian NC_000019.9 - 1399056 Apr 27, 2020 (154)
73 8.3KJPN NC_000019.9 - 1399056 Apr 27, 2021 (155)
74 TopMed NC_000019.10 - 1399057 Apr 27, 2021 (155)
75 UK 10K study - Twins NC_000019.9 - 1399056 Oct 12, 2018 (152)
76 ALFA NC_000019.10 - 1399057 Apr 27, 2021 (155)
77 ClinVar RCV000020143.3 Apr 27, 2020 (154)
78 ClinVar RCV000829815.1 Apr 27, 2020 (154)
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)
rs62128463 May 26, 2008 (130)
rs117138546 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77276008, ss90879953, ss114735065, ss168856874, ss203582292, ss210937416, ss292172855, ss1698070958 NC_000019.8:1350055:C:T NC_000019.10:1399056:C:T (self)
75413181, 41802200, 29542030, 3704667, 4711255, 12728188, 1666213, 18624682, 44686476, 607207, 16068782, 19526725, 39601001, 10545819, 84308787, 41802200, ss228006602, ss237576925, ss491143739, ss533099609, ss565805750, ss661657849, ss713457212, ss994007984, ss1081709065, ss1362047405, ss1428310443, ss1578524058, ss1637424161, ss1680418194, ss1693227220, ss1711491447, ss1937484803, ss2029517818, ss2158029465, ss2389088499, ss2702633200, ss2743414770, ss2749998640, ss2959554880, ss3016954379, ss3352158661, ss3627870712, ss3646526251, ss3683803782, ss3742783917, ss3755718135, ss3825209209, ss3835308902, ss3887584021, ss3937509082, ss3984137272, ss3986765764, ss5226339480 NC_000019.9:1399055:C:T NC_000019.10:1399056:C:T (self)
RCV000020143.3, RCV000829815.1, 531822373, 37017354, 175317611, 281017362, 4385837146, ss179362391, ss2223672969, ss3028591498, ss3285840722, ss3702177895, ss3820972332, ss3980639353, ss5065471698, ss5237243937 NC_000019.10:1399056:C:T NC_000019.10:1399056:C:T (self)
ss137513171 NT_011255.14:1339055:C:T NC_000019.10:1399056:C:T (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 rs55776826
PMID Title Author Year Journal
11978605 Denaturing gradient gel electrophoresis for the molecular characterization of six patients with guanidinoacetate methyltransferase deficiency. Item CB et al. 2002 Clinical chemistry
15108290 Characterization of seven novel mutations in seven patients with GAMT deficiency. Item CB et al. 2004 Human mutation
20301745 Creatine Deficiency Disorders Mercimek-Andrews S et al. 1993 GeneReviews®
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.post676+237644a