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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.

rs1800728

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr1:94011395 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.00024 (58/245662, GnomAD)
G=0.00032 (40/125568, TOPMED)
G=0.00022 (27/121030, ExAC) (+ 4 more)
G=0.0002 (5/30866, GnomAD)
G=0.0002 (3/13006, GO-ESP)
G=0.000 (0/3854, ALSPAC)
G=0.000 (1/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ABCA4 : Intron Variant
Publications
17 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 1 NC_000001.11:g.94011395A>G
GRCh37.p13 chr 1 NC_000001.10:g.94476951A>G
ABCA4 RefSeqGene NG_009073.1:g.114755T>C
Gene: ABCA4, ATP binding cassette subfamily A member 4 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ABCA4 transcript NM_000350.2: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.

Allele: G (allele ID: 98777 )
ClinVar Accession Disease Names Clinical Significance
RCV000008366.3 Cone-rod dystrophy 3 Pathogenic
RCV000078669.5 not provided Pathogenic
RCV000177965.6 Stargardt disease 1 Pathogenic
RCV000210325.1 Bull's eye maculopathy Likely-Pathogenic
RCV000210327.2 Retinal dystrophy Likely-Pathogenic
RCV000504857.1 Macular dystrophy Likely-Pathogenic
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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
The Genome Aggregation Database Global Study-wide 245662 A=0.99976 G=0.00024
The Genome Aggregation Database European Sub 133490 A=0.99958 G=0.00042
The Genome Aggregation Database Asian Sub 48024 A=1.0000 G=0.0000
The Genome Aggregation Database American Sub 33570 A=1.0000 G=0.0000
The Genome Aggregation Database African Sub 15282 A=0.9999 G=0.0001
The Genome Aggregation Database Ashkenazi Jewish Sub 9820 A=1.000 G=0.000
The Genome Aggregation Database Other Sub 5476 A=1.000 G=0.000
Trans-Omics for Precision Medicine Global Study-wide 125568 A=0.99968 G=0.00032
The Genome Aggregation Database Global Study-wide 30866 A=0.9998 G=0.0002
The Genome Aggregation Database European Sub 18440 A=0.9998 G=0.0002
The Genome Aggregation Database African Sub 8686 A=1.000 G=0.000
The Genome Aggregation Database East Asian Sub 1620 A=1.000 G=0.000
The Genome Aggregation Database Other Sub 980 A=1.00 G=0.00
The Genome Aggregation Database American Sub 838 A=1.00 G=0.00
The Genome Aggregation Database Ashkenazi Jewish Sub 302 A=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 13006 A=0.9998 G=0.0002
GO Exome Sequencing Project European American Sub 8600 A=1.000 G=0.000
GO Exome Sequencing Project African American Sub 4406 A=1.000 G=0.000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=1.000 G=0.000
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=1.000 G=0.000
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 Note
GRCh38.p7 chr 1 NC_000001.11:g.94011395A= NC_000001.11:g.94011395A>G
GRCh37.p13 chr 1 NC_000001.10:g.94476951A= NC_000001.10:g.94476951A>G
ABCA4 RefSeqGene NG_009073.1:g.114755T= NG_009073.1:g.114755T>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#.

7 Frequency, 16 SubSNP, 6 ClinVar submissions
No Submitter Submission ID Date (Build)
1 HGBASE ss2420853 Nov 14, 2000 (89)
2 CLINSEQ_SNP ss491598468 May 04, 2012 (137)
3 RISN-LSDB ss562069745 Dec 21, 2012 (137)
4 NHLBI-ESP ss712325256 Apr 25, 2013 (138)
5 EVA_UK10K_ALSPAC ss1600733502 Apr 01, 2015 (144)
6 EVA_UK10K_TWINSUK ss1643727535 Apr 01, 2015 (144)
7 EVA_EXAC ss1685644221 Apr 01, 2015 (144)
8 HUMAN_LONGEVITY ss2164703290 Dec 20, 2016 (150)
9 TOPMED ss2327045623 Dec 20, 2016 (150)
10 GNOMAD ss2731648379 Nov 08, 2017 (151)
11 GNOMAD ss2746375838 Nov 08, 2017 (151)
12 GNOMAD ss2758196285 Nov 08, 2017 (151)
13 AFFY ss2984867700 Nov 08, 2017 (151)
14 SWEGEN ss2987244927 Nov 08, 2017 (151)
15 ILLUMINA ss3021110724 Nov 08, 2017 (151)
16 TOPMED ss3083635711 Nov 08, 2017 (151)
17 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 94476951 Jul 19, 2018 (151)
18 The Exome Aggregation Consortium NC_000001.10 - 94476951 Jul 19, 2018 (151)
19 The Genome Aggregation Database NC_000001.10 - 94476951 Jul 19, 2018 (151)
20 The Genome Aggregation Database NC_000001.10 - 94476951 Jul 19, 2018 (151)
21 GO Exome Sequencing Project NC_000001.10 - 94476951 Jul 19, 2018 (151)
22 Trans-Omics for Precision Medicine NC_000001.11 - 94011395 Jul 19, 2018 (151)
23 UK 10K study - Twins NC_000001.10 - 94476951 Jul 19, 2018 (151)
24 ClinVar RCV000008366.3 Jul 19, 2018 (151)
25 ClinVar RCV000078669.5 Jul 19, 2018 (151)
26 ClinVar RCV000177965.6 Jul 19, 2018 (151)
27 ClinVar RCV000210325.1 Jul 19, 2018 (151)
28 ClinVar RCV000210327.2 Jul 19, 2018 (151)
29 ClinVar RCV000504857.1 Jul 19, 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).

Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss491598468 NC_000001.9:94249538:A= NC_000001.11:94011394:A= (self)
1492665, 4849667, 7595484, 663114, 90865, 1492665, ss712325256, ss1600733502, ss1643727535, ss1685644221, ss2327045623, ss2731648379, ss2746375838, ss2758196285, ss2984867700, ss2987244927, ss3021110724 NC_000001.10:94476950:A= NC_000001.11:94011394:A= (self)
14423019, ss562069745, ss2164703290, ss3083635711 NC_000001.11:94011394:A= NC_000001.11:94011394:A= (self)
ss2420853 NT_032977.9:64448868:A= NC_000001.11:94011394:A= (self)
ss491598468 NC_000001.9:94249538:A>G NC_000001.11:94011394:A>G (self)
1492665, 4849667, 7595484, 663114, 90865, 1492665, ss712325256, ss1600733502, ss1643727535, ss1685644221, ss2327045623, ss2731648379, ss2746375838, ss2758196285, ss2984867700, ss2987244927, ss3021110724 NC_000001.10:94476950:A>G NC_000001.11:94011394:A>G (self)
RCV000008366.3, RCV000078669.5, RCV000177965.6, RCV000210325.1, RCV000210327.2, RCV000504857.1, 14423019, ss562069745, ss2164703290, ss3083635711 NC_000001.11:94011394:A>G NC_000001.11:94011394:A>G (self)
ss2420853 NT_032977.9:64448868:A>G NC_000001.11:94011394: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.

17 citations for rs1800728
PMID Title Author Year Journal
10958763 A comprehensive survey of sequence variation in the ABCA4 (ABCR) gene in Stargardt disease and age-related macular degeneration. Rivera A et al. 2000 American journal of human genetics
15614537 The spectrum of retinal phenotypes caused by mutations in the ABCA4 gene. Klevering BJ et al. 2005 Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie
18285826 ABCA4 gene analysis in patients with autosomal recessive cone and cone rod dystrophies. Kitiratschky VB et al. 2008 European journal of human genetics
19074458 ABCA4 disease progression and a proposed strategy for gene therapy. Cideciyan AV et al. 2009 Human molecular genetics
20696155 Loss of peripapillary sparing in non-group I Stargardt disease. Burke TR et al. 2010 Experimental eye research
22264887 Clinical course, genetic etiology, and visual outcome in cone and cone-rod dystrophy. Thiadens AA et al. 2012 Ophthalmology
22328824 Stargardt macular dystrophy: common ABCA4 mutations in South Africa--establishment of a rapid genetic test and relating risk to patients. Roberts LJ et al. 2012 Molecular vision
23591405 Panel-based next generation sequencing as a reliable and efficient technique to detect mutations in unselected patients with retinal dystrophies. Glöckle N et al. 2014 European journal of human genetics
23695285 Stargardt disease: towards developing a model to predict phenotype. Heathfield L et al. 2013 European journal of human genetics
23757202 Free the data: one laboratory's approach to knowledge-based genomic variant classification and preparation for EMR integration of genomic data. Bean LJ et al. 2013 Human mutation
24713488 Generalized choriocapillaris dystrophy, a distinct phenotype in the spectrum of ABCA4-associated retinopathies. Bertelsen M et al. 2014 Investigative ophthalmology & visual science
25082885 Molecular diagnostic testing by eyeGENE: analysis of patients with hereditary retinal dystrophy phenotypes involving central vision loss. Alapati A et al. 2014 Investigative ophthalmology & visual science
25097241 Dependable and efficient clinical utility of target capture-based deep sequencing in molecular diagnosis of retinitis pigmentosa. Wang J et al. 2014 Investigative ophthalmology & visual science
25525159 RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Xiong HY et al. 2015 Science (New York, N.Y.)
26261413 Reduced macular function in ABCA4 carriers. Kjellström U et al. 2015 Molecular vision
26872967 Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease. Ellingford JM et al. 2016 Ophthalmology
28118664 Mutation Spectrum of the ABCA4 Gene in 335 Stargardt Disease Patients From a Multicenter German Cohort-Impact of Selected Deep Intronic Variants and Common SNPs. Schulz HL et al. 2017 Investigative ophthalmology & visual science

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