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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs6813183

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr4:61903413 (GRCh38.p7) 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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.33874 (42535/125568, TOPMED)
G=0.3189 (9822/30796, GnomAD)
G=0.387 (1937/5008, 1000G) (+ 2 more)
G=0.284 (1095/3854, ALSPAC)
G=0.266 (988/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ADGRL3 : Intron Variant
Publications
5 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.p7 chr 4 NC_000004.12:g.61903413G>C
GRCh37.p13 chr 4 NC_000004.11:g.62769131G>C
ADGRL3 RefSeqGene NG_033950.2:g.707158G>C
Gene: ADGRL3, adhesion G protein-coupled receptor L3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ADGRL3 transcript variant 3 NM_001322246.1:c. N/A Intron Variant
ADGRL3 transcript variant 1 NM_001322402.1:c. N/A Intron Variant
ADGRL3 transcript variant 2 NM_015236.5:c. N/A Intron Variant
ADGRL3 transcript variant X4 XM_011531788.2:c. N/A Intron Variant
ADGRL3 transcript variant X11 XM_011531791.2:c. N/A Intron Variant
ADGRL3 transcript variant X1 XM_017007929.1:c. N/A Intron Variant
ADGRL3 transcript variant X2 XM_017007930.1:c. N/A Intron Variant
ADGRL3 transcript variant X3 XM_017007931.1:c. N/A Intron Variant
ADGRL3 transcript variant X5 XM_017007932.1:c. N/A Intron Variant
ADGRL3 transcript variant X6 XM_017007933.1:c. N/A Intron Variant
ADGRL3 transcript variant X7 XM_017007934.1:c. N/A Intron Variant
ADGRL3 transcript variant X8 XM_017007935.1:c. N/A Intron Variant
ADGRL3 transcript variant X9 XM_017007936.1:c. N/A Intron Variant
ADGRL3 transcript variant X10 XM_017007937.1:c. N/A Intron Variant
ADGRL3 transcript variant X12 XM_017007938.1:c. N/A Intron Variant
ADGRL3 transcript variant X13 XM_017007939.1:c. N/A Intron Variant
ADGRL3 transcript variant X14 XM_017007940.1:c. N/A Intron Variant
ADGRL3 transcript variant X15 XM_017007941.1:c. N/A Intron Variant
ADGRL3 transcript variant X16 XM_017007942.1:c. 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
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
Trans-Omics for Precision Medicine Global Study-wide 125568 G=0.33874 C=0.66126
The Genome Aggregation Database Global Study-wide 30796 G=0.3189 C=0.6811
The Genome Aggregation Database European Sub 18382 G=0.2759 C=0.7241
The Genome Aggregation Database African Sub 8700 G=0.383 C=0.617
The Genome Aggregation Database East Asian Sub 1610 G=0.435 C=0.565
The Genome Aggregation Database Other Sub 972 G=0.29 C=0.71
The Genome Aggregation Database American Sub 832 G=0.41 C=0.59
The Genome Aggregation Database Ashkenazi Jewish Sub 300 G=0.30 C=0.70
1000Genomes Global Study-wide 5008 G=0.387 C=0.613
1000Genomes African Sub 1322 G=0.412 C=0.588
1000Genomes East Asian Sub 1008 G=0.465 C=0.535
1000Genomes Europe Sub 1006 G=0.288 C=0.712
1000Genomes South Asian Sub 978 G=0.38 C=0.62
1000Genomes American Sub 694 G=0.37 C=0.63
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.284 C=0.716
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.266 C=0.734
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= C Note
GRCh38.p7 chr 4 NC_000004.12:g.61903413G= NC_000004.12:g.61903413G>C
GRCh37.p13 chr 4 NC_000004.11:g.62769131G= NC_000004.11:g.62769131G>C
ADGRL3 RefSeqGene NG_033950.2:g.707158G= NG_033950.2:g.707158G>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#.

5 Frequency, 48 SubSNP submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10105758 Jul 11, 2003 (116)
2 CSHL-HAPMAP ss19570931 Feb 27, 2004 (120)
3 SSAHASNP ss22148613 Apr 05, 2004 (121)
4 HGSV ss82875947 Dec 15, 2007 (130)
5 BCMHGSC_JDW ss92605410 Mar 24, 2008 (129)
6 HUMANGENOME_JCVI ss98964474 Feb 06, 2009 (130)
7 BGI ss105830919 Feb 06, 2009 (130)
8 1000GENOMES ss107969427 Jan 22, 2009 (130)
9 1000GENOMES ss112332204 Jan 25, 2009 (130)
10 ILLUMINA-UK ss117012996 Feb 14, 2009 (130)
11 ENSEMBL ss134676045 Dec 01, 2009 (131)
12 GMI ss157335358 Dec 01, 2009 (131)
13 COMPLETE_GENOMICS ss162162423 Jul 04, 2010 (132)
14 COMPLETE_GENOMICS ss163504509 Jul 04, 2010 (132)
15 COMPLETE_GENOMICS ss166649579 Jul 04, 2010 (132)
16 BUSHMAN ss198583678 Jul 04, 2010 (132)
17 BCM-HGSC-SUB ss206365302 Jul 04, 2010 (132)
18 1000GENOMES ss220949318 Jul 14, 2010 (132)
19 1000GENOMES ss232409918 Jul 14, 2010 (132)
20 1000GENOMES ss239700219 Jul 15, 2010 (132)
21 BL ss253177701 May 09, 2011 (134)
22 GMI ss277738444 May 04, 2012 (137)
23 GMI ss284916968 Apr 25, 2013 (138)
24 PJP ss293082256 May 09, 2011 (134)
25 TISHKOFF ss557544304 Apr 25, 2013 (138)
26 SSMP ss651344833 Apr 25, 2013 (138)
27 EVA-GONL ss980159842 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1071571038 Aug 21, 2014 (142)
29 1000GENOMES ss1309906387 Aug 21, 2014 (142)
30 DDI ss1429896575 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1580574900 Apr 01, 2015 (144)
32 EVA_DECODE ss1589660380 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1610172242 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1653166275 Apr 01, 2015 (144)
35 HAMMER_LAB ss1801514205 Sep 08, 2015 (146)
36 WEILL_CORNELL_DGM ss1923399902 Feb 12, 2016 (147)
37 GENOMED ss1969751608 Jul 19, 2016 (147)
38 JJLAB ss2022284822 Sep 14, 2016 (149)
39 USC_VALOUEV ss2150411306 Dec 20, 2016 (150)
40 HUMAN_LONGEVITY ss2263232136 Dec 20, 2016 (150)
41 TOPMED ss2430959976 Dec 20, 2016 (150)
42 SYSTEMSBIOZJU ss2625641874 Nov 08, 2017 (151)
43 GRF ss2705879750 Nov 08, 2017 (151)
44 GNOMAD ss2809784512 Nov 08, 2017 (151)
45 SWEGEN ss2994770107 Nov 08, 2017 (151)
46 BIOINF_KMB_FNS_UNIBA ss3024914626 Nov 08, 2017 (151)
47 CSHL ss3345736778 Nov 08, 2017 (151)
48 TOPMED ss3430184984 Nov 08, 2017 (151)
49 1000Genomes NC_000004.11 - 62769131 Jul 20, 2018 (151)
50 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 62769131 Jul 20, 2018 (151)
51 The Genome Aggregation Database NC_000004.11 - 62769131 Jul 20, 2018 (151)
52 Trans-Omics for Precision Medicine NC_000004.12 - 61903413 Jul 20, 2018 (151)
53 UK 10K study - Twins NC_000004.11 - 62769131 Jul 20, 2018 (151)
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)
rs60557652 May 26, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss82875947 NC_000004.9:62597896:G= NC_000004.12:61903412:G= (self)
ss92605410, ss107969427, ss112332204, ss117012996, ss162162423, ss163504509, ss166649579, ss198583678, ss206365302, ss253177701, ss277738444, ss284916968, ss293082256, ss1589660380 NC_000004.10:62451725:G= NC_000004.12:61903412:G= (self)
21307718, 11853981, 150412267, 11853981, ss220949318, ss232409918, ss239700219, ss557544304, ss651344833, ss980159842, ss1071571038, ss1309906387, ss1429896575, ss1580574900, ss1610172242, ss1653166275, ss1801514205, ss1923399902, ss1969751608, ss2022284822, ss2150411306, ss2430959976, ss2625641874, ss2705879750, ss2809784512, ss2994770107, ss3345736778 NC_000004.11:62769130:G= NC_000004.12:61903412:G= (self)
282957685, ss2263232136, ss3024914626, ss3430184984 NC_000004.12:61903412:G= NC_000004.12:61903412:G= (self)
ss10105758 NT_022778.13:2972399:G= NC_000004.12:61903412:G= (self)
ss19570931, ss22148613 NT_022778.14:2972399:G= NC_000004.12:61903412:G= (self)
ss98964474, ss105830919, ss134676045, ss157335358 NT_022778.16:2979797:G= NC_000004.12:61903412:G= (self)
ss82875947 NC_000004.9:62597896:G>C NC_000004.12:61903412:G>C (self)
ss92605410, ss107969427, ss112332204, ss117012996, ss162162423, ss163504509, ss166649579, ss198583678, ss206365302, ss253177701, ss277738444, ss284916968, ss293082256, ss1589660380 NC_000004.10:62451725:G>C NC_000004.12:61903412:G>C (self)
21307718, 11853981, 150412267, 11853981, ss220949318, ss232409918, ss239700219, ss557544304, ss651344833, ss980159842, ss1071571038, ss1309906387, ss1429896575, ss1580574900, ss1610172242, ss1653166275, ss1801514205, ss1923399902, ss1969751608, ss2022284822, ss2150411306, ss2430959976, ss2625641874, ss2705879750, ss2809784512, ss2994770107, ss3345736778 NC_000004.11:62769130:G>C NC_000004.12:61903412:G>C (self)
282957685, ss2263232136, ss3024914626, ss3430184984 NC_000004.12:61903412:G>C NC_000004.12:61903412:G>C (self)
ss10105758 NT_022778.13:2972399:G>C NC_000004.12:61903412:G>C (self)
ss19570931, ss22148613 NT_022778.14:2972399:G>C NC_000004.12:61903412:G>C (self)
ss98964474, ss105830919, ss134676045, ss157335358 NT_022778.16:2979797:G>C NC_000004.12:61903412: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.

5 citations for rs6813183
PMID Title Author Year Journal
22105624 The genetics of attention deficit/hyperactivity disorder in adults, a review. Franke B et al. 2012 Molecular psychiatry
22832519 A two-locus genetic interaction between LPHN3 and 11q predicts ADHD severity and long-term outcome. Acosta MT et al. 2011 Translational psychiatry
25989180 LPHN3 and attention-deficit/hyperactivity disorder: a susceptibility and pharmacogenetic study. Bruxel EM et al. 2015 Genes, brain, and behavior
26746237 Attention deficit hyperactivity disorder: genetic association study in a cohort of Spanish children. Gomez-Sanchez CI et al. 2016 Behavioral and brain functions
28871191 Pharmacogenetics of methylphenidate in childhood attention-deficit/hyperactivity disorder: long-term effects. Gomez-Sanchez CI et al. 2017 Scientific reports

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: 0.1.4.post833+d3ba21e