Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs116416205

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:7778136 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000072 (19/264690, TOPMED)
G=0.000048 (12/251448, GnomAD_exome)
G=0.000036 (5/140248, GnomAD) (+ 7 more)
G=0.000049 (6/121402, ExAC)
G=0.00004 (1/23408, ALFA)
G=0.00008 (1/13006, GO-ESP)
G=0.0002 (1/5008, 1000G)
G=0.0000 (0/3854, ALSPAC)
G=0.0005 (2/3708, TWINSUK)
G=0.001 (1/998, GoNL)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
VAMP3 : Missense 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 1 NC_000001.11:g.7778136A>G
GRCh37.p13 chr 1 NC_000001.10:g.7838196A>G
Gene: VAMP3, vesicle associated membrane protein 3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
VAMP3 transcript NM_004781.4:c.250A>G T [ACT] > A [GCT] Coding Sequence Variant
vesicle-associated membrane protein 3 NP_004772.1:p.Thr84Ala T (Thr) > A (Ala) Missense Variant
VAMP3 transcript variant X1 XM_017002841.2:c.250A>G T [ACT] > A [GCT] Coding Sequence Variant
vesicle-associated membrane protein 3 isoform X1 XP_016858330.1:p.Thr84Ala T (Thr) > A (Ala) 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.

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 23408 A=0.99996 G=0.00004
European Sub 15886 A=0.99994 G=0.00006
African Sub 3540 A=1.0000 G=0.0000
African Others Sub 122 A=1.000 G=0.000
African American Sub 3418 A=1.0000 G=0.0000
Asian Sub 168 A=1.000 G=0.000
East Asian Sub 112 A=1.000 G=0.000
Other Asian Sub 56 A=1.00 G=0.00
Latin American 1 Sub 146 A=1.000 G=0.000
Latin American 2 Sub 610 A=1.000 G=0.000
South Asian Sub 98 A=1.00 G=0.00
Other Sub 2960 A=1.0000 G=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 A=0.999928 G=0.000072
gnomAD - Exomes Global Study-wide 251448 A=0.999952 G=0.000048
gnomAD - Exomes European Sub 135372 A=0.999919 G=0.000081
gnomAD - Exomes Asian Sub 49008 A=1.00000 G=0.00000
gnomAD - Exomes American Sub 34592 A=1.00000 G=0.00000
gnomAD - Exomes African Sub 16256 A=0.99994 G=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10080 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6140 A=1.0000 G=0.0000
gnomAD - Genomes Global Study-wide 140248 A=0.999964 G=0.000036
gnomAD - Genomes European Sub 75950 A=0.99995 G=0.00005
gnomAD - Genomes African Sub 42038 A=0.99998 G=0.00002
gnomAD - Genomes American Sub 13654 A=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3132 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2152 A=1.0000 G=0.0000
ExAC Global Study-wide 121402 A=0.999951 G=0.000049
ExAC Europe Sub 73348 A=0.99992 G=0.00008
ExAC Asian Sub 25164 A=1.00000 G=0.00000
ExAC American Sub 11578 A=1.00000 G=0.00000
ExAC African Sub 10404 A=1.00000 G=0.00000
ExAC Other Sub 908 A=1.000 G=0.000
GO Exome Sequencing Project Global Study-wide 13006 A=0.99992 G=0.00008
GO Exome Sequencing Project European American Sub 8600 A=0.9999 G=0.0001
GO Exome Sequencing Project African American Sub 4406 A=1.0000 G=0.0000
1000Genomes Global Study-wide 5008 A=0.9998 G=0.0002
1000Genomes African Sub 1322 A=1.0000 G=0.0000
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=1.000 G=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=1.0000 G=0.0000
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.9995 G=0.0005
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.999 G=0.001
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.p13 chr 1 NC_000001.11:g.7778136= NC_000001.11:g.7778136A>G
GRCh37.p13 chr 1 NC_000001.10:g.7838196= NC_000001.10:g.7838196A>G
VAMP3 transcript NM_004781.4:c.250= NM_004781.4:c.250A>G
VAMP3 transcript NM_004781.3:c.250= NM_004781.3:c.250A>G
VAMP3 transcript variant X1 XM_017002841.2:c.250= XM_017002841.2:c.250A>G
vesicle-associated membrane protein 3 NP_004772.1:p.Thr84= NP_004772.1:p.Thr84Ala
vesicle-associated membrane protein 3 isoform X1 XP_016858330.1:p.Thr84= XP_016858330.1:p.Thr84Ala
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#.

18 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217314407 Jul 14, 2010 (132)
2 1000GENOMES ss488650204 May 04, 2012 (137)
3 NHLBI-ESP ss712270198 Apr 25, 2013 (138)
4 EVA-GONL ss974830670 Aug 21, 2014 (142)
5 1000GENOMES ss1289582612 Aug 21, 2014 (142)
6 EVA_DECODE ss1584188840 Apr 01, 2015 (144)
7 EVA_UK10K_ALSPAC ss1599496386 Apr 01, 2015 (144)
8 EVA_UK10K_TWINSUK ss1642490419 Apr 01, 2015 (144)
9 EVA_EXAC ss1685278117 Apr 01, 2015 (144)
10 HUMAN_LONGEVITY ss2159837467 Dec 20, 2016 (150)
11 TOPMED ss2321995466 Dec 20, 2016 (150)
12 GNOMAD ss2731082323 Nov 08, 2017 (151)
13 SWEGEN ss2986254784 Nov 08, 2017 (151)
14 TOPMED ss3067923807 Nov 08, 2017 (151)
15 EVA_DECODE ss3686112458 Jul 12, 2019 (153)
16 EVA ss3823554509 Apr 25, 2020 (154)
17 GNOMAD ss3987885962 Apr 27, 2021 (155)
18 TOPMED ss4438361477 Apr 27, 2021 (155)
19 1000Genomes NC_000001.10 - 7838196 Oct 11, 2018 (152)
20 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 7838196 Oct 11, 2018 (152)
21 ExAC NC_000001.10 - 7838196 Oct 11, 2018 (152)
22 gnomAD - Genomes NC_000001.11 - 7778136 Apr 27, 2021 (155)
23 gnomAD - Exomes NC_000001.10 - 7838196 Jul 12, 2019 (153)
24 GO Exome Sequencing Project NC_000001.10 - 7838196 Oct 11, 2018 (152)
25 Genome of the Netherlands Release 5 NC_000001.10 - 7838196 Apr 25, 2020 (154)
26 TopMed NC_000001.11 - 7778136 Apr 27, 2021 (155)
27 UK 10K study - Twins NC_000001.10 - 7838196 Oct 11, 2018 (152)
28 ALFA NC_000001.11 - 7778136 Apr 27, 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
ss217314407, ss1584188840 NC_000001.9:7760782:A:G NC_000001.11:7778135:A:G (self)
254815, 128948, 4455585, 96840, 13240, 55971, 128948, ss488650204, ss712270198, ss974830670, ss1289582612, ss1599496386, ss1642490419, ss1685278117, ss2321995466, ss2731082323, ss2986254784, ss3823554509 NC_000001.10:7838195:A:G NC_000001.11:7778135:A:G (self)
1752606, 1234806, 1967812, 11327100251, ss2159837467, ss3067923807, ss3686112458, ss3987885962, ss4438361477 NC_000001.11:7778135:A:G NC_000001.11:7778135: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 rs116416205

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