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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.

rs3816511

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr17:17506087 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.464789 (123025/264690, TOPMED)
G=0.439238 (61496/140006, GnomAD)
G=0.35785 (11807/32994, ALFA) (+ 15 more)
A=0.32848 (5502/16750, 8.3KJPN)
A=0.3984 (1995/5008, 1000G)
G=0.2712 (1215/4480, Estonian)
G=0.2535 (977/3854, ALSPAC)
G=0.2584 (958/3708, TWINSUK)
A=0.3125 (915/2928, KOREAN)
A=0.3089 (561/1816, Korea1K)
G=0.264 (263/998, GoNL)
G=0.228 (137/600, NorthernSweden)
A=0.086 (46/534, MGP)
G=0.330 (115/348, SGDP_PRJ)
A=0.431 (93/216, Qatari)
A=0.208 (44/212, Vietnamese)
G=0.26 (12/46, Siberian)
G=0.12 (5/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PEMT : Intron 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 17 NC_000017.11:g.17506087G>A
GRCh38.p13 chr 17 NC_000017.11:g.17506087G>C
GRCh37.p13 chr 17 NC_000017.10:g.17409401G>A
GRCh37.p13 chr 17 NC_000017.10:g.17409401G>C
Gene: PEMT, phosphatidylethanolamine N-methyltransferase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PEMT transcript variant 4 NM_001267551.2:c.587+140C…

NM_001267551.2:c.587+140C>T

N/A Intron Variant
PEMT transcript variant 5 NM_001267552.2:c.684+140C…

NM_001267552.2:c.684+140C>T

N/A Intron Variant
PEMT transcript variant 2 NM_007169.3:c.542+140C>T N/A Intron Variant
PEMT transcript variant 1 NM_148172.3:c.653+140C>T N/A Intron Variant
PEMT transcript variant 3 NM_148173.2:c.542+140C>T N/A Intron Variant
PEMT transcript variant X1 XM_006721418.4:c.590+140C…

XM_006721418.4:c.590+140C>T

N/A Intron Variant
PEMT transcript variant X3 XM_017024016.1:c.320+140C…

XM_017024016.1:c.320+140C>T

N/A Intron Variant
PEMT transcript variant X2 XM_024450532.1:c.542+140C…

XM_024450532.1:c.542+140C>T

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.

Not Reported in ClinVar

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 32994 G=0.35785 A=0.64215, C=0.00000
European Sub 20976 G=0.28089 A=0.71911, C=0.00000
African Sub 3132 G=0.7187 A=0.2813, C=0.0000
African Others Sub 118 G=0.729 A=0.271, C=0.000
African American Sub 3014 G=0.7183 A=0.2817, C=0.0000
Asian Sub 142 G=0.711 A=0.289, C=0.000
East Asian Sub 108 G=0.685 A=0.315, C=0.000
Other Asian Sub 34 G=0.79 A=0.21, C=0.00
Latin American 1 Sub 304 G=0.484 A=0.516, C=0.000
Latin American 2 Sub 5198 G=0.4586 A=0.5414, C=0.0000
South Asian Sub 136 G=0.449 A=0.551, C=0.000
Other Sub 3106 G=0.3126 A=0.6874, C=0.0000


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=0.464789 A=0.535211
gnomAD - Genomes Global Study-wide 140006 G=0.439238 A=0.560762
gnomAD - Genomes European Sub 75800 G=0.27806 A=0.72194
gnomAD - Genomes African Sub 41960 G=0.70405 A=0.29595
gnomAD - Genomes American Sub 13652 G=0.45437 A=0.54563
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.3893 A=0.6107
gnomAD - Genomes East Asian Sub 3118 G=0.7835 A=0.2165
gnomAD - Genomes Other Sub 2152 G=0.4354 A=0.5646
8.3KJPN JAPANESE Study-wide 16750 G=0.67152 A=0.32848
1000Genomes Global Study-wide 5008 G=0.6016 A=0.3984
1000Genomes African Sub 1322 G=0.7859 A=0.2141
1000Genomes East Asian Sub 1008 G=0.7907 A=0.2093
1000Genomes Europe Sub 1006 G=0.3121 A=0.6879
1000Genomes South Asian Sub 978 G=0.561 A=0.439
1000Genomes American Sub 694 G=0.452 A=0.548
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.2712 A=0.7288
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.2535 A=0.7465
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.2584 A=0.7416
KOREAN population from KRGDB KOREAN Study-wide 2928 G=0.6875 A=0.3125, C=0.0000
Korean Genome Project KOREAN Study-wide 1816 G=0.6911 A=0.3089
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.264 A=0.736
Northern Sweden ACPOP Study-wide 600 G=0.228 A=0.772
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.914 A=0.086
SGDP_PRJ Global Study-wide 348 G=0.330 A=0.670
Qatari Global Study-wide 216 G=0.569 A=0.431
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.792 A=0.208
Siberian Global Study-wide 46 G=0.26 A=0.74
The Danish reference pan genome Danish Study-wide 40 G=0.12 A=0.88
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
GRCh38.p13 chr 17 NC_000017.11:g.17506087= NC_000017.11:g.17506087G>A NC_000017.11:g.17506087G>C
GRCh37.p13 chr 17 NC_000017.10:g.17409401= NC_000017.10:g.17409401G>A NC_000017.10:g.17409401G>C
PEMT transcript variant 4 NM_001267551.1:c.587+140= NM_001267551.1:c.587+140C>T NM_001267551.1:c.587+140C>G
PEMT transcript variant 4 NM_001267551.2:c.587+140= NM_001267551.2:c.587+140C>T NM_001267551.2:c.587+140C>G
PEMT transcript variant 5 NM_001267552.1:c.684+140= NM_001267552.1:c.684+140C>T NM_001267552.1:c.684+140C>G
PEMT transcript variant 5 NM_001267552.2:c.684+140= NM_001267552.2:c.684+140C>T NM_001267552.2:c.684+140C>G
PEMT transcript variant 2 NM_007169.2:c.542+140= NM_007169.2:c.542+140C>T NM_007169.2:c.542+140C>G
PEMT transcript variant 2 NM_007169.3:c.542+140= NM_007169.3:c.542+140C>T NM_007169.3:c.542+140C>G
PEMT transcript variant 1 NM_148172.2:c.653+140= NM_148172.2:c.653+140C>T NM_148172.2:c.653+140C>G
PEMT transcript variant 1 NM_148172.3:c.653+140= NM_148172.3:c.653+140C>T NM_148172.3:c.653+140C>G
PEMT transcript variant 3 NM_148173.1:c.542+140= NM_148173.1:c.542+140C>T NM_148173.1:c.542+140C>G
PEMT transcript variant 3 NM_148173.2:c.542+140= NM_148173.2:c.542+140C>T NM_148173.2:c.542+140C>G
PEMT transcript variant X2 XM_005256410.1:c.320+140= XM_005256410.1:c.320+140C>T XM_005256410.1:c.320+140C>G
PEMT transcript variant X1 XM_006721418.4:c.590+140= XM_006721418.4:c.590+140C>T XM_006721418.4:c.590+140C>G
PEMT transcript variant X3 XM_017024016.1:c.320+140= XM_017024016.1:c.320+140C>T XM_017024016.1:c.320+140C>G
PEMT transcript variant X2 XM_024450532.1:c.542+140= XM_024450532.1:c.542+140C>T XM_024450532.1:c.542+140C>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#.

75 SubSNP, 18 Frequency submissions
No Submitter Submission ID Date (Build)
1 YUSUKE ss5002924 Aug 28, 2002 (107)
2 RIKENSNPRC ss6311505 Feb 20, 2003 (111)
3 CSHL-HAPMAP ss16745162 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss19364486 Feb 27, 2004 (120)
5 SSAHASNP ss21431022 Apr 05, 2004 (121)
6 PERLEGEN ss23643159 Sep 20, 2004 (123)
7 ABI ss44021341 Mar 14, 2006 (126)
8 BCMHGSC_JDW ss90550978 Mar 24, 2008 (129)
9 EGP_SNPS ss95215836 Feb 05, 2009 (130)
10 HUMANGENOME_JCVI ss96538978 Feb 05, 2009 (130)
11 BGI ss103335697 Dec 01, 2009 (131)
12 ENSEMBL ss136610108 Dec 01, 2009 (131)
13 ENSEMBL ss137002558 Dec 01, 2009 (131)
14 ILLUMINA ss152536488 Dec 01, 2009 (131)
15 GMI ss157892882 Dec 01, 2009 (131)
16 ILLUMINA ss159102648 Dec 01, 2009 (131)
17 ILLUMINA ss159846007 Dec 01, 2009 (131)
18 COMPLETE_GENOMICS ss167906220 Jul 04, 2010 (132)
19 ILLUMINA ss168871122 Jul 04, 2010 (132)
20 BUSHMAN ss202306860 Jul 04, 2010 (132)
21 1000GENOMES ss227490643 Jul 14, 2010 (132)
22 1000GENOMES ss237202499 Jul 15, 2010 (132)
23 1000GENOMES ss243510029 Jul 15, 2010 (132)
24 BL ss255530682 May 09, 2011 (134)
25 GMI ss282712848 May 04, 2012 (137)
26 PJP ss292024704 May 09, 2011 (134)
27 ILLUMINA ss479154462 Sep 08, 2015 (146)
28 TISHKOFF ss565201274 Apr 25, 2013 (138)
29 SSMP ss660992998 Apr 25, 2013 (138)
30 ILLUMINA ss832615444 Aug 21, 2014 (142)
31 ILLUMINA ss833206133 Aug 21, 2014 (142)
32 EVA-GONL ss992977768 Aug 21, 2014 (142)
33 1000GENOMES ss1358110054 Aug 21, 2014 (142)
34 DDI ss1427994244 Apr 01, 2015 (144)
35 EVA_GENOME_DK ss1578111694 Apr 01, 2015 (144)
36 EVA_UK10K_ALSPAC ss1635392215 Apr 01, 2015 (144)
37 EVA_UK10K_TWINSUK ss1678386248 Apr 01, 2015 (144)
38 EVA_DECODE ss1697019589 Apr 01, 2015 (144)
39 EVA_MGP ss1711450787 Apr 01, 2015 (144)
40 WEILL_CORNELL_DGM ss1936429874 Feb 12, 2016 (147)
41 JJLAB ss2029001621 Sep 14, 2016 (149)
42 USC_VALOUEV ss2157453213 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2215891111 Dec 20, 2016 (150)
44 TOPMED ss2380785486 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2628995096 Nov 08, 2017 (151)
46 GRF ss2702001574 Nov 08, 2017 (151)
47 GNOMAD ss2948266790 Nov 08, 2017 (151)
48 AFFY ss2985726483 Nov 08, 2017 (151)
49 SWEGEN ss3015283718 Nov 08, 2017 (151)
50 BIOINF_KMB_FNS_UNIBA ss3028320996 Nov 08, 2017 (151)
51 TOPMED ss3258570365 Nov 08, 2017 (151)
52 TOPMED ss3258570366 Nov 08, 2017 (151)
53 CSHL ss3351677938 Nov 08, 2017 (151)
54 ILLUMINA ss3636358037 Oct 12, 2018 (152)
55 ILLUMINA ss3638152886 Oct 12, 2018 (152)
56 URBANLAB ss3650615773 Oct 12, 2018 (152)
57 EGCUT_WGS ss3682240936 Jul 13, 2019 (153)
58 EVA_DECODE ss3700187891 Jul 13, 2019 (153)
59 ACPOP ss3741919632 Jul 13, 2019 (153)
60 EVA ss3754514162 Jul 13, 2019 (153)
61 PACBIO ss3788164108 Jul 13, 2019 (153)
62 PACBIO ss3793130199 Jul 13, 2019 (153)
63 PACBIO ss3798015875 Jul 13, 2019 (153)
64 KHV_HUMAN_GENOMES ss3819788158 Jul 13, 2019 (153)
65 EVA ss3834807795 Apr 27, 2020 (154)
66 EVA ss3841012894 Apr 27, 2020 (154)
67 EVA ss3846507734 Apr 27, 2020 (154)
68 SGDP_PRJ ss3885453426 Apr 27, 2020 (154)
69 KRGDB ss3935062162 Apr 27, 2020 (154)
70 KOGIC ss3978509329 Apr 27, 2020 (154)
71 FSA-LAB ss3984109567 Apr 26, 2021 (155)
72 EVA ss3986716285 Apr 26, 2021 (155)
73 TOPMED ss5031133825 Apr 26, 2021 (155)
74 TOMMO_GENOMICS ss5221733088 Apr 26, 2021 (155)
75 EVA ss5237238004 Apr 26, 2021 (155)
76 1000Genomes NC_000017.10 - 17409401 Oct 12, 2018 (152)
77 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 17409401 Oct 12, 2018 (152)
78 Genetic variation in the Estonian population NC_000017.10 - 17409401 Oct 12, 2018 (152)
79 The Danish reference pan genome NC_000017.10 - 17409401 Apr 27, 2020 (154)
80 gnomAD - Genomes NC_000017.11 - 17506087 Apr 26, 2021 (155)
81 Genome of the Netherlands Release 5 NC_000017.10 - 17409401 Apr 27, 2020 (154)
82 KOREAN population from KRGDB NC_000017.10 - 17409401 Apr 27, 2020 (154)
83 Korean Genome Project NC_000017.11 - 17506087 Apr 27, 2020 (154)
84 Medical Genome Project healthy controls from Spanish population NC_000017.10 - 17409401 Apr 27, 2020 (154)
85 Northern Sweden NC_000017.10 - 17409401 Jul 13, 2019 (153)
86 Qatari NC_000017.10 - 17409401 Apr 27, 2020 (154)
87 SGDP_PRJ NC_000017.10 - 17409401 Apr 27, 2020 (154)
88 Siberian NC_000017.10 - 17409401 Apr 27, 2020 (154)
89 8.3KJPN NC_000017.10 - 17409401 Apr 26, 2021 (155)
90 TopMed NC_000017.11 - 17506087 Apr 26, 2021 (155)
91 UK 10K study - Twins NC_000017.10 - 17409401 Oct 12, 2018 (152)
92 A Vietnamese Genetic Variation Database NC_000017.10 - 17409401 Jul 13, 2019 (153)
93 ALFA NC_000017.11 - 17506087 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss90550978, ss167906220, ss202306860, ss255530682, ss282712848, ss292024704, ss1697019589 NC_000017.9:17350125:G:A NC_000017.11:17506086:G:A (self)
71332170, 39559837, 27979184, 4315706, 17636640, 42239556, 566547, 15204497, 18471796, 37470406, 9969567, 79702395, 39559837, 8763856, ss227490643, ss237202499, ss243510029, ss479154462, ss565201274, ss660992998, ss832615444, ss833206133, ss992977768, ss1358110054, ss1427994244, ss1578111694, ss1635392215, ss1678386248, ss1711450787, ss1936429874, ss2029001621, ss2157453213, ss2380785486, ss2628995096, ss2702001574, ss2948266790, ss2985726483, ss3015283718, ss3351677938, ss3636358037, ss3638152886, ss3682240936, ss3741919632, ss3754514162, ss3788164108, ss3793130199, ss3798015875, ss3834807795, ss3841012894, ss3885453426, ss3935062162, ss3984109567, ss3986716285, ss5221733088 NC_000017.10:17409400:G:A NC_000017.11:17506086:G:A (self)
502900759, 34887330, 153970626, 246679487, 3607811286, ss2215891111, ss3028320996, ss3258570365, ss3650615773, ss3700187891, ss3819788158, ss3846507734, ss3978509329, ss5031133825, ss5237238004 NC_000017.11:17506086:G:A NC_000017.11:17506086:G:A (self)
ss16745162, ss19364486, ss21431022 NT_010718.14:16250406:G:A NC_000017.11:17506086:G:A (self)
ss5002924, ss6311505, ss23643159, ss44021341, ss95215836, ss96538978, ss103335697, ss136610108, ss137002558, ss152536488, ss157892882, ss159102648, ss159846007, ss168871122 NT_010718.16:17012774:G:A NC_000017.11:17506086:G:A (self)
42239556, ss3935062162 NC_000017.10:17409400:G:C NC_000017.11:17506086:G:C (self)
3607811286, ss3258570366 NC_000017.11:17506086:G:C NC_000017.11:17506086: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.

No publications for rs3816511

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