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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.

rs753281850

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:17484 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000726 (115/158418, GnomAD_exome)
A=0.001602 (223/139190, GnomAD)
A=0.00178 (45/25320, ALFA) (+ 3 more)
A=0.00293 (59/20166, ExAC)
A=0.00030 (5/16758, 8.3KJPN)
A=0.002 (1/534, MGP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MIR6859-1 : 2KB Upstream Variant
WASH7P : Intron 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.17484G>A
GRCh37.p13 chr 1 NC_000001.10:g.17484G>A
Gene: WASH7P, WASP family homolog 7, pseudogene (minus strand)
Molecule type Change Amino acid[Codon] SO Term
WASH7P transcript NR_024540.1:n. N/A Intron Variant
Gene: MIR6859-1, microRNA 6859-1 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
MIR6859-1 transcript NR_106918.1:n. N/A Upstream 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

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 25320 G=0.99822 A=0.00178
European Sub 18142 G=0.99868 A=0.00132
African Sub 3410 G=0.9965 A=0.0035
African Others Sub 116 G=1.000 A=0.000
African American Sub 3294 G=0.9964 A=0.0036
Asian Sub 164 G=1.000 A=0.000
East Asian Sub 110 G=1.000 A=0.000
Other Asian Sub 54 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 94 G=1.00 A=0.00
Other Sub 2754 G=0.9967 A=0.0033


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
gnomAD - Exomes Global Study-wide 158418 G=0.999274 A=0.000726
gnomAD - Exomes European Sub 78672 G=0.99886 A=0.00114
gnomAD - Exomes Asian Sub 34144 G=0.99979 A=0.00021
gnomAD - Exomes American Sub 24760 G=0.99980 A=0.00020
gnomAD - Exomes Ashkenazi Jewish Sub 8506 G=1.0000 A=0.0000
gnomAD - Exomes African Sub 7836 G=0.9983 A=0.0017
gnomAD - Exomes Other Sub 4500 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 139190 G=0.998398 A=0.001602
gnomAD - Genomes European Sub 75394 G=0.99829 A=0.00171
gnomAD - Genomes African Sub 41586 G=0.99810 A=0.00190
gnomAD - Genomes American Sub 13610 G=0.99912 A=0.00088
gnomAD - Genomes Ashkenazi Jewish Sub 3322 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2144 G=0.9986 A=0.0014
Allele Frequency Aggregator Total Global 25320 G=0.99822 A=0.00178
Allele Frequency Aggregator European Sub 18142 G=0.99868 A=0.00132
Allele Frequency Aggregator African Sub 3410 G=0.9965 A=0.0035
Allele Frequency Aggregator Other Sub 2754 G=0.9967 A=0.0033
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 164 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 94 G=1.00 A=0.00
ExAC Global Study-wide 20166 G=0.99707 A=0.00293
ExAC Europe Sub 9476 G=0.9969 A=0.0031
ExAC Asian Sub 8442 G=0.9983 A=0.0017
ExAC African Sub 1552 G=0.9903 A=0.0097
ExAC American Sub 460 G=0.998 A=0.002
ExAC Other Sub 236 G=1.000 A=0.000
8.3KJPN JAPANESE Study-wide 16758 G=0.99970 A=0.00030
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.998 A=0.002
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
GRCh38.p13 chr 1 NC_000001.11:g.17484= NC_000001.11:g.17484G>A
GRCh37.p13 chr 1 NC_000001.10:g.17484= NC_000001.10:g.17484G>A
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#.

9 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1685216874 Apr 01, 2015 (144)
2 EVA_MGP ss1710883264 Apr 01, 2015 (144)
3 GNOMAD ss2730985495 Nov 08, 2017 (151)
4 GNOMAD ss2746168715 Nov 08, 2017 (151)
5 GNOMAD ss2750602001 Nov 08, 2017 (151)
6 SWEGEN ss2986141488 Nov 08, 2017 (151)
7 TOPMED ss3066317590 Nov 08, 2017 (151)
8 EVA_DECODE ss3685990290 Jul 12, 2019 (153)
9 TOMMO_GENOMICS ss5142031547 Apr 25, 2021 (155)
10 ExAC NC_000001.10 - 17484 Oct 11, 2018 (152)
11 gnomAD - Genomes NC_000001.11 - 17484 Apr 25, 2021 (155)
12 gnomAD - Exomes NC_000001.10 - 17484 Jul 12, 2019 (153)
13 Medical Genome Project healthy controls from Spanish population NC_000001.10 - 17484 Apr 25, 2020 (154)
14 8.3KJPN NC_000001.10 - 17484 Apr 25, 2021 (155)
15 ALFA NC_000001.11 - 17484 Apr 25, 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
4389945, 86, 16, 854, ss1685216874, ss1710883264, ss2730985495, ss2746168715, ss2750602001, ss2986141488, ss5142031547 NC_000001.10:17483:G:A NC_000001.11:17483:G:A (self)
1692, 2120983745, ss3066317590, ss3685990290 NC_000001.11:17483:G:A NC_000001.11:17483:G:A (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 rs753281850

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