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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.

rs587748117

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:150647567-150647572 (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
dupC
Variation Type
Indel Insertion and Deletion
Frequency
dupC=0.001375 (364/264690, TOPMED)
dupC=0.001418 (198/139658, GnomAD)
dupC=0.00021 (6/28256, 14KJPN) (+ 3 more)
dupC=0.00006 (1/16760, 8.3KJPN)
dupC=0.00078 (11/14050, ALFA)
dupC=0.0008 (4/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GOLPH3L : 3 Prime UTR 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 14050 CCCCCC=0.99922 CCCCCCC=0.00078
European Sub 9690 CCCCCC=1.0000 CCCCCCC=0.0000
African Sub 2898 CCCCCC=0.9962 CCCCCCC=0.0038
African Others Sub 114 CCCCCC=1.000 CCCCCCC=0.000
African American Sub 2784 CCCCCC=0.9960 CCCCCCC=0.0040
Asian Sub 112 CCCCCC=1.000 CCCCCCC=0.000
East Asian Sub 86 CCCCCC=1.00 CCCCCCC=0.00
Other Asian Sub 26 CCCCCC=1.00 CCCCCCC=0.00
Latin American 1 Sub 146 CCCCCC=1.000 CCCCCCC=0.000
Latin American 2 Sub 610 CCCCCC=1.000 CCCCCCC=0.000
South Asian Sub 98 CCCCCC=1.00 CCCCCCC=0.00
Other Sub 496 CCCCCC=1.000 CCCCCCC=0.000


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 -

No frequency provided

dupC=0.001375
gnomAD - Genomes Global Study-wide 139658 -

No frequency provided

dupC=0.001418
gnomAD - Genomes European Sub 75664 -

No frequency provided

dupC=0.00001
gnomAD - Genomes African Sub 41832 -

No frequency provided

dupC=0.00447
gnomAD - Genomes American Sub 13572 -

No frequency provided

dupC=0.00074
gnomAD - Genomes Ashkenazi Jewish Sub 3322 -

No frequency provided

dupC=0.0000
gnomAD - Genomes East Asian Sub 3126 -

No frequency provided

dupC=0.0000
gnomAD - Genomes Other Sub 2142 -

No frequency provided

dupC=0.0000
14KJPN JAPANESE Study-wide 28256 -

No frequency provided

dupC=0.00021
8.3KJPN JAPANESE Study-wide 16760 -

No frequency provided

dupC=0.00006
Allele Frequency Aggregator Total Global 14050 (C)6=0.99922 dupC=0.00078
Allele Frequency Aggregator European Sub 9690 (C)6=1.0000 dupC=0.0000
Allele Frequency Aggregator African Sub 2898 (C)6=0.9962 dupC=0.0038
Allele Frequency Aggregator Latin American 2 Sub 610 (C)6=1.000 dupC=0.000
Allele Frequency Aggregator Other Sub 496 (C)6=1.000 dupC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 (C)6=1.000 dupC=0.000
Allele Frequency Aggregator Asian Sub 112 (C)6=1.000 dupC=0.000
Allele Frequency Aggregator South Asian Sub 98 (C)6=1.00 dupC=0.00
1000Genomes Global Study-wide 5008 -

No frequency provided

dupC=0.0008
1000Genomes African Sub 1322 -

No frequency provided

dupC=0.0030
1000Genomes East Asian Sub 1008 -

No frequency provided

dupC=0.0000
1000Genomes Europe Sub 1006 -

No frequency provided

dupC=0.0000
1000Genomes South Asian Sub 978 -

No frequency provided

dupC=0.000
1000Genomes American Sub 694 -

No frequency provided

dupC=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 1 NC_000001.11:g.150647572dup
GRCh37.p13 chr 1 NC_000001.10:g.150620048dup
Gene: GOLPH3L, golgi phosphoprotein 3 like (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GOLPH3L transcript NM_018178.6:c.*749_*754= N/A 3 Prime UTR Variant
GOLPH3L transcript variant X1 XM_006711428.3:c.*749_*75…

XM_006711428.3:c.*749_*754=

N/A 3 Prime UTR Variant
GOLPH3L transcript variant X2 XM_047424285.1:c.*749_*75…

XM_047424285.1:c.*749_*754=

N/A 3 Prime UTR Variant
GOLPH3L transcript variant X3 XM_047424286.1:c. N/A Genic Downstream 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 (C)6= dupC
GRCh38.p14 chr 1 NC_000001.11:g.150647567_150647572= NC_000001.11:g.150647572dup
GRCh37.p13 chr 1 NC_000001.10:g.150620043_150620048= NC_000001.10:g.150620048dup
GOLPH3L transcript NM_018178.6:c.*749_*754= NM_018178.6:c.*754dup
GOLPH3L transcript NM_018178.5:c.*749_*754= NM_018178.5:c.*754dup
GOLPH3L transcript variant X1 XM_006711428.3:c.*749_*754= XM_006711428.3:c.*754dup
GOLPH3L transcript variant X1 XM_006711428.2:c.*749_*754= XM_006711428.2:c.*754dup
GOLPH3L transcript variant X1 XM_006711428.1:c.*749_*754= XM_006711428.1:c.*754dup
GOLPH3L transcript variant X2 XM_047424285.1:c.*749_*754= XM_047424285.1:c.*754dup
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#.

6 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1367845405 Aug 28, 2014 (142)
2 GNOMAD ss2761001469 Nov 08, 2017 (151)
3 TOPMED ss4467348124 Apr 25, 2021 (155)
4 TOMMO_GENOMICS ss5146352746 Apr 25, 2021 (155)
5 TOMMO_GENOMICS ss5673505810 Oct 12, 2022 (156)
6 EVA ss5910140612 Oct 12, 2022 (156)
7 1000Genomes NC_000001.10 - 150620043 Oct 11, 2018 (152)
8 gnomAD - Genomes NC_000001.11 - 150647567 Apr 25, 2021 (155)
9 8.3KJPN NC_000001.10 - 150620043 Apr 25, 2021 (155)
10 14KJPN NC_000001.11 - 150647567 Oct 12, 2022 (156)
11 TopMed NC_000001.11 - 150647567 Apr 25, 2021 (155)
12 ALFA NC_000001.11 - 150647567 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
3607257, 4322053, ss1367845405, ss2761001469, ss5146352746 NC_000001.10:150620042::C NC_000001.11:150647566:CCCCCC:CCCC…

NC_000001.11:150647566:CCCCCC:CCCCCCC

(self)
26248793, 7342914, 30954459, ss4467348124, ss5673505810, ss5910140612 NC_000001.11:150647566::C NC_000001.11:150647566:CCCCCC:CCCC…

NC_000001.11:150647566:CCCCCC:CCCCCCC

(self)
14060406924 NC_000001.11:150647566:CCCCCC:CCCC…

NC_000001.11:150647566:CCCCCC:CCCCCCC

NC_000001.11:150647566:CCCCCC:CCCC…

NC_000001.11:150647566:CCCCCC:CCCCCCC

(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 rs587748117

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