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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.

rs1487851536

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:183098009-183098017 (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
delAGA
Variation Type
Indel Insertion and Deletion
Frequency
delAGA=0.000011 (3/264690, TOPMED)
delAGA=0.000007 (1/140280, GnomAD)
delAGA=0.00003 (1/35894, GnomAD_exome) (+ 4 more)
delAGA=0.00004 (1/28256, 14KJPN)
delAGA=0.00006 (1/16758, 8.3KJPN)
delAGA=0.00008 (1/11862, ALFA)
delAGA=0.0002 (1/6404, 1000G_30x)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
WWC2-AS2 : Non Coding Transcript Variant
WWC2 : 2KB Upstream 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 11862 AGAAGAAGA=0.99992 AGAAGA=0.00008 0.999831 0.0 0.000169 0
European Sub 7618 AGAAGAAGA=0.9999 AGAAGA=0.0001 0.999737 0.0 0.000263 0
African Sub 2816 AGAAGAAGA=1.0000 AGAAGA=0.0000 1.0 0.0 0.0 N/A
African Others Sub 108 AGAAGAAGA=1.000 AGAAGA=0.000 1.0 0.0 0.0 N/A
African American Sub 2708 AGAAGAAGA=1.0000 AGAAGA=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 AGAAGAAGA=1.000 AGAAGA=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 AGAAGAAGA=1.00 AGAAGA=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 AGAAGAAGA=1.00 AGAAGA=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 AGAAGAAGA=1.000 AGAAGA=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 AGAAGAAGA=1.000 AGAAGA=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 AGAAGAAGA=1.00 AGAAGA=0.00 1.0 0.0 0.0 N/A
Other Sub 470 AGAAGAAGA=1.000 AGAAGA=0.000 1.0 0.0 0.0 N/A


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 (AGA)3=0.999989 delAGA=0.000011
gnomAD - Genomes Global Study-wide 140280 (AGA)3=0.999993 delAGA=0.000007
gnomAD - Genomes European Sub 75944 (AGA)3=0.99999 delAGA=0.00001
gnomAD - Genomes African Sub 42066 (AGA)3=1.00000 delAGA=0.00000
gnomAD - Genomes American Sub 13662 (AGA)3=1.00000 delAGA=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 (AGA)3=1.0000 delAGA=0.0000
gnomAD - Genomes East Asian Sub 3130 (AGA)3=1.0000 delAGA=0.0000
gnomAD - Genomes Other Sub 2154 (AGA)3=1.0000 delAGA=0.0000
gnomAD - Exomes Global Study-wide 35894 (AGA)3=0.99997 delAGA=0.00003
gnomAD - Exomes European Sub 19144 (AGA)3=0.99995 delAGA=0.00005
gnomAD - Exomes Asian Sub 6464 (AGA)3=1.0000 delAGA=0.0000
gnomAD - Exomes American Sub 4974 (AGA)3=1.0000 delAGA=0.0000
gnomAD - Exomes African Sub 3078 (AGA)3=1.0000 delAGA=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 1282 (AGA)3=1.0000 delAGA=0.0000
gnomAD - Exomes Other Sub 952 (AGA)3=1.000 delAGA=0.000
14KJPN JAPANESE Study-wide 28256 (AGA)3=0.99996 delAGA=0.00004
8.3KJPN JAPANESE Study-wide 16758 (AGA)3=0.99994 delAGA=0.00006
Allele Frequency Aggregator Total Global 11862 (AGA)3=0.99992 delAGA=0.00008
Allele Frequency Aggregator European Sub 7618 (AGA)3=0.9999 delAGA=0.0001
Allele Frequency Aggregator African Sub 2816 (AGA)3=1.0000 delAGA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 (AGA)3=1.000 delAGA=0.000
Allele Frequency Aggregator Other Sub 470 (AGA)3=1.000 delAGA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (AGA)3=1.000 delAGA=0.000
Allele Frequency Aggregator Asian Sub 108 (AGA)3=1.000 delAGA=0.000
Allele Frequency Aggregator South Asian Sub 94 (AGA)3=1.00 delAGA=0.00
1000Genomes_30x Global Study-wide 6404 (AGA)3=0.9998 delAGA=0.0002
1000Genomes_30x African Sub 1786 (AGA)3=0.9994 delAGA=0.0006
1000Genomes_30x Europe Sub 1266 (AGA)3=1.0000 delAGA=0.0000
1000Genomes_30x South Asian Sub 1202 (AGA)3=1.0000 delAGA=0.0000
1000Genomes_30x East Asian Sub 1170 (AGA)3=1.0000 delAGA=0.0000
1000Genomes_30x American Sub 980 (AGA)3=1.000 delAGA=0.000
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 4 NC_000004.12:g.183098009AGA[2]
GRCh37.p13 chr 4 NC_000004.11:g.184019162AGA[2]
WWC2 RefSeqGene NG_051586.1:g.4375AGA[2]
LOC121056750 genomic region NG_074142.1:g.94AGA[2]
Gene: WWC2, WW and C2 domain containing 2 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
WWC2 transcript variant 2 NM_024949.6:c. N/A Upstream Transcript Variant
WWC2 transcript variant X1 XM_011532269.4:c. N/A Upstream Transcript Variant
WWC2 transcript variant X1 XM_024454225.2:c. N/A Upstream Transcript Variant
WWC2 transcript variant X2 XM_047416198.1:c. N/A Upstream Transcript Variant
WWC2 transcript variant X3 XM_047416199.1:c. N/A Upstream Transcript Variant
Gene: WWC2-AS2, WWC2 antisense RNA 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WWC2-AS2 transcript NR_024008.1:n.1183TCT[2] N/A Non Coding 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 (AGA)3= delAGA
GRCh38.p14 chr 4 NC_000004.12:g.183098009_183098017= NC_000004.12:g.183098009AGA[2]
GRCh37.p13 chr 4 NC_000004.11:g.184019162_184019170= NC_000004.11:g.184019162AGA[2]
WWC2 RefSeqGene NG_051586.1:g.4375_4383= NG_051586.1:g.4375AGA[2]
LOC121056750 genomic region NG_074142.1:g.94_102= NG_074142.1:g.94AGA[2]
C4orf38 transcript NM_153008.3:c.571_579= NM_153008.3:c.571TCT[2]
FLJ30277 transcript NM_153008.2:c.571_579= NM_153008.2:c.571TCT[2]
WWC2-AS2 transcript NR_024008.1:n.1183_1191= NR_024008.1:n.1183TCT[2]
FLJ30277 transcript NM_153008.1:c.571_579= NM_153008.1:c.571TCT[2]
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 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2734838052 Nov 08, 2017 (151)
2 GNOMAD ss4096984947 Apr 26, 2021 (155)
3 TOPMED ss4645107374 Apr 26, 2021 (155)
4 TOMMO_GENOMICS ss5169712412 Apr 26, 2021 (155)
5 1000G_HIGH_COVERAGE ss5545170795 Oct 17, 2022 (156)
6 SANFORD_IMAGENETICS ss5636878007 Oct 17, 2022 (156)
7 TOMMO_GENOMICS ss5705171931 Oct 17, 2022 (156)
8 1000Genomes_30x NC_000004.12 - 183098009 Oct 17, 2022 (156)
9 gnomAD - Genomes NC_000004.12 - 183098009 Apr 26, 2021 (155)
10 gnomAD - Exomes NC_000004.11 - 184019162 Jul 13, 2019 (153)
11 8.3KJPN NC_000004.11 - 184019162 Apr 26, 2021 (155)
12 14KJPN NC_000004.12 - 183098009 Oct 17, 2022 (156)
13 TopMed NC_000004.12 - 183098009 Apr 26, 2021 (155)
14 ALFA NC_000004.12 - 183098009 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
3951296, 27681719, ss2734838052, ss5169712412, ss5636878007 NC_000004.11:184019161:AGA: NC_000004.12:183098008:AGAAGAAGA:A…

NC_000004.12:183098008:AGAAGAAGA:AGAAGA

(self)
32696730, 175979789, 39009035, 482484930, ss4096984947, ss4645107374, ss5545170795, ss5705171931 NC_000004.12:183098008:AGA: NC_000004.12:183098008:AGAAGAAGA:A…

NC_000004.12:183098008:AGAAGAAGA:AGAAGA

(self)
11808690640 NC_000004.12:183098008:AGAAGAAGA:A…

NC_000004.12:183098008:AGAAGAAGA:AGAAGA

NC_000004.12:183098008:AGAAGAAGA:A…

NC_000004.12:183098008:AGAAGAAGA:AGAAGA

(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 rs1487851536

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