Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs116532931

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr17:17528006 (GRCh38.p14) 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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.021115 (5589/264690, TOPMED)
G=0.020069 (2814/140214, GnomAD)
G=0.01560 (225/14420, ALFA) (+ 7 more)
G=0.0209 (134/6404, 1000G_30x)
G=0.0202 (101/5008, 1000G)
G=0.0003 (1/3854, ALSPAC)
G=0.0005 (2/3708, TWINSUK)
G=0.019 (4/216, Qatari)
A=0.5 (4/8, SGDP_PRJ)
G=0.5 (4/8, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PEMT : Intron Variant
Publications
0 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 14420 A=0.98440 G=0.01560 0.969626 0.000832 0.029542 6
European Sub 9824 A=0.9995 G=0.0005 0.998982 0.0 0.001018 0
African Sub 2946 A=0.9291 G=0.0709 0.862186 0.004073 0.133741 0
African Others Sub 114 A=0.974 G=0.026 0.947368 0.0 0.052632 0
African American Sub 2832 A=0.9273 G=0.0727 0.858757 0.004237 0.137006 0
Asian Sub 112 A=1.000 G=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 A=0.986 G=0.014 0.972603 0.0 0.027397 0
Latin American 2 Sub 610 A=0.993 G=0.007 0.986885 0.0 0.013115 0
South Asian Sub 98 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Sub 684 A=0.993 G=0.007 0.98538 0.0 0.01462 0


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 A=0.978885 G=0.021115
gnomAD - Genomes Global Study-wide 140214 A=0.979931 G=0.020069
gnomAD - Genomes European Sub 75936 A=0.99976 G=0.00024
gnomAD - Genomes African Sub 42010 A=0.93678 G=0.06322
gnomAD - Genomes American Sub 13660 A=0.99224 G=0.00776
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3134 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2152 A=0.9842 G=0.0158
Allele Frequency Aggregator Total Global 14420 A=0.98440 G=0.01560
Allele Frequency Aggregator European Sub 9824 A=0.9995 G=0.0005
Allele Frequency Aggregator African Sub 2946 A=0.9291 G=0.0709
Allele Frequency Aggregator Other Sub 684 A=0.993 G=0.007
Allele Frequency Aggregator Latin American 2 Sub 610 A=0.993 G=0.007
Allele Frequency Aggregator Latin American 1 Sub 146 A=0.986 G=0.014
Allele Frequency Aggregator Asian Sub 112 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
1000Genomes_30x Global Study-wide 6404 A=0.9791 G=0.0209
1000Genomes_30x African Sub 1786 A=0.9272 G=0.0728
1000Genomes_30x Europe Sub 1266 A=0.9992 G=0.0008
1000Genomes_30x South Asian Sub 1202 A=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=0.997 G=0.003
1000Genomes Global Study-wide 5008 A=0.9798 G=0.0202
1000Genomes African Sub 1322 A=0.9259 G=0.0741
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=0.9990 G=0.0010
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=0.997 G=0.003
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.9997 G=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9995 G=0.0005
Qatari Global Study-wide 216 A=0.981 G=0.019
SGDP_PRJ Global Study-wide 8 A=0.5 G=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.p14 chr 17 NC_000017.11:g.17528006A>G
GRCh37.p13 chr 17 NC_000017.10:g.17431320A>G
Gene: PEMT, phosphatidylethanolamine N-methyltransferase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PEMT transcript variant 4 NM_001267551.2:c.139-5611…

NM_001267551.2:c.139-5611T>C

 		N/A Intron Variant
PEMT transcript variant 5 NM_001267552.2:c.205-5611…

NM_001267552.2:c.205-5611T>C

 		N/A Intron Variant
PEMT transcript variant 2 NM_007169.3:c.94-5611T>C N/A Intron Variant
PEMT transcript variant 1 NM_148172.3:c.205-5611T>C N/A Intron Variant
PEMT transcript variant 3 NM_148173.2:c.94-5611T>C N/A Intron Variant
PEMT transcript variant X1 XM_006721418.5:c.220-5611…

XM_006721418.5:c.220-5611T>C

 		N/A Intron Variant
PEMT transcript variant X3 XM_024450532.2:c.94-5611T…

XM_024450532.2:c.94-5611T>C

 		N/A Intron Variant
PEMT transcript variant X2 XM_017024016.2:c. N/A Genic 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.

Not Reported in ClinVar
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 A= G
GRCh38.p14 chr 17 NC_000017.11:g.17528006= NC_000017.11:g.17528006A>G
GRCh37.p13 chr 17 NC_000017.10:g.17431320= NC_000017.10:g.17431320A>G
PEMT transcript variant 4 NM_001267551.1:c.139-5611= NM_001267551.1:c.139-5611T>C
PEMT transcript variant 4 NM_001267551.2:c.139-5611= NM_001267551.2:c.139-5611T>C
PEMT transcript variant 5 NM_001267552.1:c.205-5611= NM_001267552.1:c.205-5611T>C
PEMT transcript variant 5 NM_001267552.2:c.205-5611= NM_001267552.2:c.205-5611T>C
PEMT transcript variant 2 NM_007169.2:c.94-5611= NM_007169.2:c.94-5611T>C
PEMT transcript variant 2 NM_007169.3:c.94-5611= NM_007169.3:c.94-5611T>C
PEMT transcript variant 1 NM_148172.2:c.205-5611= NM_148172.2:c.205-5611T>C
PEMT transcript variant 1 NM_148172.3:c.205-5611= NM_148172.3:c.205-5611T>C
PEMT transcript variant 3 NM_148173.1:c.94-5611= NM_148173.1:c.94-5611T>C
PEMT transcript variant 3 NM_148173.2:c.94-5611= NM_148173.2:c.94-5611T>C
PEMT transcript variant X1 XM_006721418.5:c.220-5611= XM_006721418.5:c.220-5611T>C
PEMT transcript variant X3 XM_024450532.2:c.94-5611= XM_024450532.2:c.94-5611T>C
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#.

19 SubSNP, 9 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss227490743 Jul 14, 2010 (132)
2 TISHKOFF ss565201392 Apr 25, 2013 (138)
3 1000GENOMES ss1358110746 Aug 21, 2014 (142)
4 EVA_UK10K_ALSPAC ss1635392637 Apr 01, 2015 (144)
5 EVA_UK10K_TWINSUK ss1678386670 Apr 01, 2015 (144)
6 HAMMER_LAB ss1808729150 Sep 08, 2015 (146)
7 WEILL_CORNELL_DGM ss1936430069 Feb 12, 2016 (147)
8 HUMAN_LONGEVITY ss2215892656 Dec 20, 2016 (150)
9 GNOMAD ss2948268690 Nov 08, 2017 (151)
10 KHV_HUMAN_GENOMES ss3819788355 Jul 13, 2019 (153)
11 SGDP_PRJ ss3885453763 Apr 27, 2020 (154)
12 TOPMED ss5031139696 Apr 26, 2021 (155)
13 1000G_HIGH_COVERAGE ss5302612589 Oct 16, 2022 (156)
14 EVA ss5426711821 Oct 16, 2022 (156)
15 HUGCELL_USP ss5495762629 Oct 16, 2022 (156)
16 1000G_HIGH_COVERAGE ss5606046301 Oct 16, 2022 (156)
17 SANFORD_IMAGENETICS ss5659830419 Oct 16, 2022 (156)
18 EVA ss5913426131 Oct 16, 2022 (156)
19 EVA ss5951240908 Oct 16, 2022 (156)
20 1000Genomes NC_000017.10 - 17431320 Oct 12, 2018 (152)
21 1000Genomes_30x NC_000017.11 - 17528006 Oct 16, 2022 (156)
22 The Avon Longitudinal Study of Parents and Children NC_000017.10 - 17431320 Oct 12, 2018 (152)
23 gnomAD - Genomes NC_000017.11 - 17528006 Apr 26, 2021 (155)
24 Qatari NC_000017.10 - 17431320 Apr 27, 2020 (154)
25 SGDP_PRJ NC_000017.10 - 17431320 Apr 27, 2020 (154)
26 TopMed NC_000017.11 - 17528006 Apr 26, 2021 (155)
27 UK 10K study - Twins NC_000017.10 - 17431320 Oct 12, 2018 (152)
28 ALFA NC_000017.11 - 17528006 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
71332879, 39560278, 18471991, 37470743, 39560278, ss227490743, ss565201392, ss1358110746, ss1635392637, ss1678386670, ss1808729150, ss1936430069, ss2948268690, ss3885453763, ss5426711821, ss5659830419, ss5951240908 NC_000017.10:17431319:A:G NC_000017.11:17528005:A:G (self)
93572236, 502905376, 246685358, 13661575984, ss2215892656, ss3819788355, ss5031139696, ss5302612589, ss5495762629, ss5606046301, ss5913426131 NC_000017.11:17528005:A:G NC_000017.11:17528005:A:G (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 rs116532931

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.post820+afb47a3d