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

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.

rs556752953

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:20735642 (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
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00007 (2/28252, 14KJPN)
T=0.00006 (1/16756, 8.3KJPN)
A=0.0002 (1/6404, 1000G_30x) (+ 2 more)
A=0.0002 (1/5008, 1000G)
G=0.0 (0/2, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NBEAP1 : Intron Variant
LOC124905495 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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
14KJPN JAPANESE Study-wide 28252 G=0.99993 T=0.00007
8.3KJPN JAPANESE Study-wide 16756 G=0.99994 T=0.00006
1000Genomes_30x Global Study-wide 6404 G=0.9998 A=0.0002
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=1.0000 A=0.0000
1000Genomes_30x East Asian Sub 1170 G=0.9991 A=0.0009
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9998 A=0.0002
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9990 A=0.0010
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
SGDP_PRJ Global Study-wide 2 G=0.0 A=1.0
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 15 NC_000015.10:g.20735642G>A
GRCh38.p14 chr 15 NC_000015.10:g.20735642G>T
GRCh37.p13 chr 15 NC_000015.9:g.20940971G>A
GRCh37.p13 chr 15 NC_000015.9:g.20940971G>T
GRCh38.p14 chr 15 fix patch HG2365_PATCH NW_021160017.1:g.977411G>A
GRCh38.p14 chr 15 fix patch HG2365_PATCH NW_021160017.1:g.977411G>T
Gene: NBEAP1, neurobeachin pseudogene 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
NBEAP1 transcript NR_027992.1:n. 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

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= A T
GRCh38.p14 chr 15 NC_000015.10:g.20735642= NC_000015.10:g.20735642G>A NC_000015.10:g.20735642G>T
GRCh37.p13 chr 15 NC_000015.9:g.20940971= NC_000015.9:g.20940971G>A NC_000015.9:g.20940971G>T
GRCh38.p14 chr 15 fix patch HG2365_PATCH NW_021160017.1:g.977411= NW_021160017.1:g.977411G>A NW_021160017.1:g.977411G>T
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, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1352630460 Aug 21, 2014 (142)
2 SGDP_PRJ ss3882413209 Apr 27, 2020 (154)
3 VINODS ss4031578548 Apr 26, 2021 (155)
4 TOMMO_GENOMICS ss5215127198 Apr 26, 2021 (155)
5 EVA ss5417881128 Oct 16, 2022 (156)
6 1000G_HIGH_COVERAGE ss5598700008 Oct 16, 2022 (156)
7 TOMMO_GENOMICS ss5768638228 Oct 16, 2022 (156)
8 1000Genomes NC_000015.9 - 20940971 Oct 12, 2018 (152)
9 1000Genomes_30x NC_000015.10 - 20735642 Oct 16, 2022 (156)
10 SGDP_PRJ NC_000015.9 - 20940971 Apr 27, 2020 (154)
11 8.3KJPN NC_000015.9 - 20940971 Apr 26, 2021 (155)
12 14KJPN NC_000015.10 - 20735642 Oct 16, 2022 (156)
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
65670214, 34430189, ss1352630460, ss3882413209, ss5417881128 NC_000015.9:20940970:G:A NC_000015.10:20735641:G:A (self)
86225943, ss5598700008 NC_000015.10:20735641:G:A NC_000015.10:20735641:G:A
73096505, ss5215127198 NC_000015.9:20940970:G:T NC_000015.10:20735641:G:T (self)
102475332, ss4031578548, ss5768638228 NC_000015.10:20735641:G:T NC_000015.10:20735641:G:T (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 rs556752953

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.post761+d5e8e07