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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.

rs17851582

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr19:1397444 (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
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.063954 (16928/264690, TOPMED)
A=0.076346 (18891/247438, GnomAD_exome)
A=0.070102 (9830/140224, GnomAD) (+ 17 more)
A=0.088244 (11666/132202, ALFA)
A=0.075541 (8958/118584, ExAC)
A=0.03757 (2956/78680, PAGE_STUDY)
A=0.07121 (926/13004, GO-ESP)
A=0.0365 (183/5008, 1000G)
A=0.1270 (569/4480, Estonian)
A=0.1064 (410/3854, ALSPAC)
A=0.0984 (365/3708, TWINSUK)
A=0.001 (1/792, PRJEB37584)
A=0.070 (42/600, NorthernSweden)
A=0.049 (26/534, MGP)
A=0.056 (17/302, FINRISK)
A=0.032 (7/216, Qatari)
G=0.45 (20/44, SGDP_PRJ)
A=0.03 (1/40, GENOME_DK)
G=0.5 (5/10, Siberian)
A=0.5 (5/10, Siberian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
GAMT : Missense 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 132202 G=0.911756 A=0.088244
European Sub 104608 G=0.903994 A=0.096006
African Sub 4450 G=0.9791 A=0.0209
African Others Sub 124 G=1.000 A=0.000
African American Sub 4326 G=0.9785 A=0.0215
Asian Sub 3208 G=1.0000 A=0.0000
East Asian Sub 1956 G=1.0000 A=0.0000
Other Asian Sub 1252 G=1.0000 A=0.0000
Latin American 1 Sub 228 G=0.939 A=0.061
Latin American 2 Sub 4730 G=0.9220 A=0.0780
South Asian Sub 120 G=0.892 A=0.108
Other Sub 14858 G=0.92368 A=0.07632


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=0.936046 A=0.063954
gnomAD - Exomes Global Study-wide 247438 G=0.923654 A=0.076346
gnomAD - Exomes European Sub 131844 G=0.903932 A=0.096068
gnomAD - Exomes Asian Sub 48946 G=0.95722 A=0.04278
gnomAD - Exomes American Sub 34520 G=0.92158 A=0.07842
gnomAD - Exomes African Sub 16036 G=0.98366 A=0.01634
gnomAD - Exomes Ashkenazi Jewish Sub 10006 G=0.93494 A=0.06506
gnomAD - Exomes Other Sub 6086 G=0.9160 A=0.0840
gnomAD - Genomes Global Study-wide 140224 G=0.929898 A=0.070102
gnomAD - Genomes European Sub 75920 G=0.89652 A=0.10348
gnomAD - Genomes African Sub 42036 G=0.98123 A=0.01877
gnomAD - Genomes American Sub 13656 G=0.93820 A=0.06180
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9392 A=0.0608
gnomAD - Genomes East Asian Sub 3134 G=0.9997 A=0.0003
gnomAD - Genomes Other Sub 2154 G=0.9359 A=0.0641
Allele Frequency Aggregator Total Global 132202 G=0.911756 A=0.088244
Allele Frequency Aggregator European Sub 104608 G=0.903994 A=0.096006
Allele Frequency Aggregator Other Sub 14858 G=0.92368 A=0.07632
Allele Frequency Aggregator Latin American 2 Sub 4730 G=0.9220 A=0.0780
Allele Frequency Aggregator African Sub 4450 G=0.9791 A=0.0209
Allele Frequency Aggregator Asian Sub 3208 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 1 Sub 228 G=0.939 A=0.061
Allele Frequency Aggregator South Asian Sub 120 G=0.892 A=0.108
ExAC Global Study-wide 118584 G=0.924459 A=0.075541
ExAC Europe Sub 71392 G=0.90699 A=0.09301
ExAC Asian Sub 25002 G=0.95368 A=0.04632
ExAC American Sub 11416 G=0.91845 A=0.08155
ExAC African Sub 9906 G=0.9830 A=0.0170
ExAC Other Sub 868 G=0.930 A=0.070
The PAGE Study Global Study-wide 78680 G=0.96243 A=0.03757
The PAGE Study AfricanAmerican Sub 32500 G=0.97812 A=0.02188
The PAGE Study Mexican Sub 10810 G=0.92174 A=0.07826
The PAGE Study Asian Sub 8316 G=0.9995 A=0.0005
The PAGE Study PuertoRican Sub 7916 G=0.9482 A=0.0518
The PAGE Study NativeHawaiian Sub 4532 G=0.9715 A=0.0285
The PAGE Study Cuban Sub 4230 G=0.9239 A=0.0761
The PAGE Study Dominican Sub 3828 G=0.9585 A=0.0415
The PAGE Study CentralAmerican Sub 2450 G=0.9449 A=0.0551
The PAGE Study SouthAmerican Sub 1982 G=0.9445 A=0.0555
The PAGE Study NativeAmerican Sub 1260 G=0.9405 A=0.0595
The PAGE Study SouthAsian Sub 856 G=0.936 A=0.064
GO Exome Sequencing Project Global Study-wide 13004 G=0.92879 A=0.07121
GO Exome Sequencing Project European American Sub 8600 G=0.9028 A=0.0972
GO Exome Sequencing Project African American Sub 4404 G=0.9796 A=0.0204
1000Genomes Global Study-wide 5008 G=0.9635 A=0.0365
1000Genomes African Sub 1322 G=0.9970 A=0.0030
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9175 A=0.0825
1000Genomes South Asian Sub 978 G=0.948 A=0.052
1000Genomes American Sub 694 G=0.935 A=0.065
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8730 A=0.1270
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.8936 A=0.1064
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9016 A=0.0984
CNV burdens in cranial meningiomas Global Study-wide 792 G=0.999 A=0.001
CNV burdens in cranial meningiomas CRM Sub 792 G=0.999 A=0.001
Northern Sweden ACPOP Study-wide 600 G=0.930 A=0.070
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.951 A=0.049
FINRISK Finnish from FINRISK project Study-wide 302 G=0.944 A=0.056
Qatari Global Study-wide 216 G=0.968 A=0.032
SGDP_PRJ Global Study-wide 44 G=0.45 A=0.55
The Danish reference pan genome Danish Study-wide 40 G=0.97 A=0.03
Siberian Global Study-wide 10 G=0.5 A=0.5
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.1397444G>A
GRCh38.p13 chr 19 NC_000019.10:g.1397444G>T
GRCh37.p13 chr 19 NC_000019.9:g.1397443G>A
GRCh37.p13 chr 19 NC_000019.9:g.1397443G>T
NDUFS7 RefSeqGene NG_008283.1:g.18561G>A
NDUFS7 RefSeqGene NG_008283.1:g.18561G>T
GAMT RefSeqGene NG_009785.1:g.9110C>T
GAMT RefSeqGene NG_009785.1:g.9110C>A
Gene: GAMT, guanidinoacetate N-methyltransferase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GAMT transcript variant 2 NM_138924.3:c. N/A Genic Downstream Transcript Variant
GAMT transcript variant 1 NM_000156.6:c.626C>T T [ACG] > M [ATG] Coding Sequence Variant
guanidinoacetate N-methyltransferase isoform a NP_000147.1:p.Thr209Met T (Thr) > M (Met) Missense Variant
GAMT transcript variant 1 NM_000156.6:c.626C>A T [ACG] > K [AAG] Coding Sequence Variant
guanidinoacetate N-methyltransferase isoform a NP_000147.1:p.Thr209Lys T (Thr) > K (Lys) 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: 33920 )
ClinVar Accession Disease Names Clinical Significance
RCV000020144.5 Deficiency of guanidinoacetate methyltransferase Benign
RCV000117117.6 not specified Benign
RCV000272863.1 Leigh syndrome Likely-Benign
RCV000311501.1 Mitochondrial complex I deficiency Likely-Benign
RCV000676877.1 not provided Benign
RCV000715403.1 History of neurodevelopmental disorder 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 G= A T
GRCh38.p13 chr 19 NC_000019.10:g.1397444= NC_000019.10:g.1397444G>A NC_000019.10:g.1397444G>T
GRCh37.p13 chr 19 NC_000019.9:g.1397443= NC_000019.9:g.1397443G>A NC_000019.9:g.1397443G>T
NDUFS7 RefSeqGene NG_008283.1:g.18561= NG_008283.1:g.18561G>A NG_008283.1:g.18561G>T
GAMT RefSeqGene NG_009785.1:g.9110= NG_009785.1:g.9110C>T NG_009785.1:g.9110C>A
GAMT transcript variant 1 NM_000156.6:c.626= NM_000156.6:c.626C>T NM_000156.6:c.626C>A
GAMT transcript variant 1 NM_000156.5:c.626= NM_000156.5:c.626C>T NM_000156.5:c.626C>A
guanidinoacetate N-methyltransferase isoform a NP_000147.1:p.Thr209= NP_000147.1:p.Thr209Met NP_000147.1:p.Thr209Lys
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#.

76 SubSNP, 19 Frequency, 6 ClinVar submissions
No Submitter Submission ID Date (Build)
1 MGC_GENOME_DIFF ss28505884 Sep 24, 2004 (123)
2 APPLERA_GI ss48419380 Mar 14, 2006 (126)
3 BCMHGSC_JDW ss90879949 Mar 24, 2008 (129)
4 ILLUMINA ss120035935 Dec 01, 2009 (131)
5 ENSEMBL ss137513165 Dec 01, 2009 (131)
6 SEATTLESEQ ss159737817 Dec 01, 2009 (131)
7 ILLUMINA ss161062836 Dec 01, 2009 (131)
8 GENEREVIEWS ss179362390 Nov 18, 2009 (131)
9 1000GENOMES ss237576923 Jul 15, 2010 (132)
10 NHLBI-ESP ss342479089 May 09, 2011 (134)
11 ILLUMINA ss479403660 Sep 08, 2015 (146)
12 1000GENOMES ss491143737 May 04, 2012 (137)
13 EXOME_CHIP ss491535803 May 04, 2012 (137)
14 CLINSEQ_SNP ss491753203 May 04, 2012 (137)
15 ILLUMINA ss535597519 Sep 08, 2015 (146)
16 SSMP ss661657842 Apr 25, 2013 (138)
17 ILLUMINA ss780738213 Sep 08, 2015 (146)
18 ILLUMINA ss783415162 Sep 08, 2015 (146)
19 EVA-GONL ss994007976 Aug 21, 2014 (142)
20 JMKIDD_LAB ss1067581120 Aug 21, 2014 (142)
21 1000GENOMES ss1362047354 Aug 21, 2014 (142)
22 DDI ss1428310441 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1578524055 Apr 01, 2015 (144)
24 EVA_FINRISK ss1584112339 Apr 01, 2015 (144)
25 EVA_UK10K_ALSPAC ss1637424129 Apr 01, 2015 (144)
26 EVA_UK10K_TWINSUK ss1680418162 Apr 01, 2015 (144)
27 EVA_EXAC ss1693227123 Apr 01, 2015 (144)
28 EVA_DECODE ss1698070948 Apr 01, 2015 (144)
29 EVA_MGP ss1711491444 Apr 01, 2015 (144)
30 ILLUMINA ss1752274101 Sep 08, 2015 (146)
31 ILLUMINA ss1917929280 Feb 12, 2016 (147)
32 WEILL_CORNELL_DGM ss1937484792 Feb 12, 2016 (147)
33 ILLUMINA ss1946518741 Feb 12, 2016 (147)
34 ILLUMINA ss1959827080 Feb 12, 2016 (147)
35 GENOMED ss1968592248 Jul 19, 2016 (147)
36 JJLAB ss2029517813 Sep 14, 2016 (149)
37 USC_VALOUEV ss2158029458 Dec 20, 2016 (150)
38 HUMAN_LONGEVITY ss2223672840 Dec 20, 2016 (150)
39 TOPMED ss2389088378 Dec 20, 2016 (150)
40 GNOMAD ss2743414626 Nov 08, 2017 (151)
41 GNOMAD ss2749998599 Nov 08, 2017 (151)
42 GNOMAD ss2959554747 Nov 08, 2017 (151)
43 AFFY ss2985124976 Nov 08, 2017 (151)
44 SWEGEN ss3016954360 Nov 08, 2017 (151)
45 ILLUMINA ss3021867696 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3028591496 Nov 08, 2017 (151)
47 TOPMED ss3285840355 Nov 08, 2017 (151)
48 CSHL ss3352158658 Nov 08, 2017 (151)
49 ILLUMINA ss3627870708 Oct 12, 2018 (152)
50 ILLUMINA ss3627870709 Oct 12, 2018 (152)
51 ILLUMINA ss3634718212 Oct 12, 2018 (152)
52 ILLUMINA ss3636408962 Oct 12, 2018 (152)
53 ILLUMINA ss3640425520 Oct 12, 2018 (152)
54 ILLUMINA ss3644711796 Oct 12, 2018 (152)
55 OMUKHERJEE_ADBS ss3646526248 Oct 12, 2018 (152)
56 ILLUMINA ss3652291660 Oct 12, 2018 (152)
57 ILLUMINA ss3653897596 Oct 12, 2018 (152)
58 EGCUT_WGS ss3683803759 Jul 13, 2019 (153)
59 EVA_DECODE ss3702177876 Jul 13, 2019 (153)
60 ILLUMINA ss3725698035 Jul 13, 2019 (153)
61 ACPOP ss3742783909 Jul 13, 2019 (153)
62 ILLUMINA ss3744456237 Jul 13, 2019 (153)
63 ILLUMINA ss3745018284 Jul 13, 2019 (153)
64 EVA ss3755718117 Jul 13, 2019 (153)
65 PAGE_CC ss3771989029 Jul 13, 2019 (153)
66 ILLUMINA ss3772515708 Jul 13, 2019 (153)
67 KHV_HUMAN_GENOMES ss3820972320 Jul 13, 2019 (153)
68 EVA ss3825209187 Apr 27, 2020 (154)
69 EVA ss3825920122 Apr 27, 2020 (154)
70 EVA ss3835308897 Apr 27, 2020 (154)
71 SGDP_PRJ ss3887583999 Apr 27, 2020 (154)
72 FSA-LAB ss3984137269 Apr 27, 2021 (155)
73 EVA ss3984737163 Apr 27, 2021 (155)
74 EVA ss3986765753 Apr 27, 2021 (155)
75 TOPMED ss5065471203 Apr 27, 2021 (155)
76 EVA ss5236952631 Apr 27, 2021 (155)
77 1000Genomes NC_000019.9 - 1397443 Oct 12, 2018 (152)
78 The Avon Longitudinal Study of Parents and Children NC_000019.9 - 1397443 Oct 12, 2018 (152)
79 Genetic variation in the Estonian population NC_000019.9 - 1397443 Oct 12, 2018 (152)
80 ExAC NC_000019.9 - 1397443 Oct 12, 2018 (152)
81 FINRISK NC_000019.9 - 1397443 Apr 27, 2020 (154)
82 The Danish reference pan genome NC_000019.9 - 1397443 Apr 27, 2020 (154)
83 gnomAD - Genomes NC_000019.10 - 1397444 Apr 27, 2021 (155)
84 gnomAD - Exomes NC_000019.9 - 1397443 Jul 13, 2019 (153)
85 GO Exome Sequencing Project NC_000019.9 - 1397443 Oct 12, 2018 (152)
86 Medical Genome Project healthy controls from Spanish population NC_000019.9 - 1397443 Apr 27, 2020 (154)
87 Northern Sweden NC_000019.9 - 1397443 Jul 13, 2019 (153)
88 The PAGE Study NC_000019.10 - 1397444 Jul 13, 2019 (153)
89 CNV burdens in cranial meningiomas NC_000019.9 - 1397443 Apr 27, 2021 (155)
90 Qatari NC_000019.9 - 1397443 Apr 27, 2020 (154)
91 SGDP_PRJ NC_000019.9 - 1397443 Apr 27, 2020 (154)
92 Siberian NC_000019.9 - 1397443 Apr 27, 2020 (154)
93 TopMed NC_000019.10 - 1397444 Apr 27, 2021 (155)
94 UK 10K study - Twins NC_000019.9 - 1397443 Oct 12, 2018 (152)
95 ALFA NC_000019.10 - 1397444 Apr 27, 2021 (155)
96 ClinVar RCV000020144.5 Apr 27, 2021 (155)
97 ClinVar RCV000117117.6 Jul 13, 2019 (153)
98 ClinVar RCV000272863.1 Oct 12, 2018 (152)
99 ClinVar RCV000311501.1 Oct 12, 2018 (152)
100 ClinVar RCV000676877.1 Oct 12, 2018 (152)
101 ClinVar RCV000715403.1 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss90879949, ss491753203, ss1698070948 NC_000019.8:1348442:G:A NC_000019.10:1397443:G:A (self)
75413129, 41802166, 29542007, 3704564, 108800, 4711252, 12728029, 1666191, 607204, 16068774, 286715, 19526714, 39600979, 10545812, 41802166, ss237576923, ss342479089, ss479403660, ss491143737, ss491535803, ss535597519, ss661657842, ss780738213, ss783415162, ss994007976, ss1067581120, ss1362047354, ss1428310441, ss1578524055, ss1584112339, ss1637424129, ss1680418162, ss1693227123, ss1711491444, ss1752274101, ss1917929280, ss1937484792, ss1946518741, ss1959827080, ss1968592248, ss2029517813, ss2158029458, ss2389088378, ss2743414626, ss2749998599, ss2959554747, ss2985124976, ss3016954360, ss3021867696, ss3352158658, ss3627870708, ss3627870709, ss3634718212, ss3636408962, ss3640425520, ss3644711796, ss3646526248, ss3652291660, ss3653897596, ss3683803759, ss3742783909, ss3744456237, ss3745018284, ss3755718117, ss3772515708, ss3825209187, ss3825920122, ss3835308897, ss3887583999, ss3984137269, ss3984737163, ss3986765753 NC_000019.9:1397442:G:A NC_000019.10:1397443:G:A (self)
RCV000020144.5, RCV000117117.6, RCV000272863.1, RCV000311501.1, RCV000676877.1, RCV000715403.1, 531821962, 1210498, 175317292, 281016867, 11051941544, ss179362390, ss2223672840, ss3028591496, ss3285840355, ss3702177876, ss3725698035, ss3771989029, ss3820972320, ss5065471203, ss5236952631 NC_000019.10:1397443:G:A NC_000019.10:1397443:G:A (self)
ss28505884, ss48419380, ss120035935, ss137513165, ss159737817, ss161062836 NT_011255.14:1337442:G:A NC_000019.10:1397443:G:A (self)
ss2743414626 NC_000019.9:1397442:G:T NC_000019.10:1397443:G: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 rs17851582
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
20301745 Creatine Deficiency Disorders Mercimek-Andrews S et al. 1993 GeneReviews®
25741868 Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S et al. 2015 Genetics in medicine
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