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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.

rs1486015780

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:24679550-24679560 (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
del(GGT)2GCA
Variation Type
Indel Insertion and Deletion
Frequency
del(GGT)2GCA=0.000008 (2/264690, TOPMED)
del(GGT)2GCA=0.000014 (2/140168, GnomAD)
del(GGT)2GCA=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NPAP1 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 14050 CAGGTGGTGCA=1.00000 CA=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 CAGGTGGTGCA=1.0000 CA=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 CAGGTGGTGCA=1.0000 CA=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 CAGGTGGTGCA=1.000 CA=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 CAGGTGGTGCA=1.0000 CA=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 CAGGTGGTGCA=1.000 CA=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 CAGGTGGTGCA=1.00 CA=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 CAGGTGGTGCA=1.00 CA=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 CAGGTGGTGCA=1.000 CA=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 CAGGTGGTGCA=1.000 CA=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 CAGGTGGTGCA=1.00 CA=0.00 1.0 0.0 0.0 N/A
Other Sub 496 CAGGTGGTGCA=1.000 CA=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 CA(GGT)2GCA=0.999992 del(GGT)2GCA=0.000008
gnomAD - Genomes Global Study-wide 140168 CA(GGT)2GCA=0.999986 del(GGT)2GCA=0.000014
gnomAD - Genomes European Sub 75902 CA(GGT)2GCA=0.99997 del(GGT)2GCA=0.00003
gnomAD - Genomes African Sub 42018 CA(GGT)2GCA=1.00000 del(GGT)2GCA=0.00000
gnomAD - Genomes American Sub 13648 CA(GGT)2GCA=1.00000 del(GGT)2GCA=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3318 CA(GGT)2GCA=1.0000 del(GGT)2GCA=0.0000
gnomAD - Genomes East Asian Sub 3130 CA(GGT)2GCA=1.0000 del(GGT)2GCA=0.0000
gnomAD - Genomes Other Sub 2152 CA(GGT)2GCA=1.0000 del(GGT)2GCA=0.0000
Allele Frequency Aggregator Total Global 14050 CA(GGT)2GCA=1.00000 del(GGT)2GCA=0.00000
Allele Frequency Aggregator European Sub 9690 CA(GGT)2GCA=1.0000 del(GGT)2GCA=0.0000
Allele Frequency Aggregator African Sub 2898 CA(GGT)2GCA=1.0000 del(GGT)2GCA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 CA(GGT)2GCA=1.000 del(GGT)2GCA=0.000
Allele Frequency Aggregator Other Sub 496 CA(GGT)2GCA=1.000 del(GGT)2GCA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 CA(GGT)2GCA=1.000 del(GGT)2GCA=0.000
Allele Frequency Aggregator Asian Sub 112 CA(GGT)2GCA=1.000 del(GGT)2GCA=0.000
Allele Frequency Aggregator South Asian Sub 98 CA(GGT)2GCA=1.00 del(GGT)2GCA=0.00
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.24679552_24679560del
GRCh37.p13 chr 15 NC_000015.9:g.24924699_24924707del
NPAP1 RefSeqGene NG_021413.1:g.9159_9167del
Gene: NPAP1, nuclear pore associated protein 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NPAP1 transcript NM_018958.3:c.*212_*222= N/A 3 Prime UTR 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 CA(GGT)2GCA= del(GGT)2GCA
GRCh38.p14 chr 15 NC_000015.10:g.24679550_24679560= NC_000015.10:g.24679552_24679560del
GRCh37.p13 chr 15 NC_000015.9:g.24924697_24924707= NC_000015.9:g.24924699_24924707del
NPAP1 RefSeqGene NG_021413.1:g.9157_9167= NG_021413.1:g.9159_9167del
NPAP1 transcript NM_018958.3:c.*212_*222= NM_018958.3:c.*214_*222del
NPAP1 transcript NM_018958.2:c.*212_*222= NM_018958.2:c.*214_*222del
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#.

2 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss4285496999 Apr 27, 2021 (155)
2 TOPMED ss4984849820 Apr 27, 2021 (155)
3 gnomAD - Genomes NC_000015.10 - 24679550 Apr 27, 2021 (155)
4 TopMed NC_000015.10 - 24679550 Apr 27, 2021 (155)
5 ALFA NC_000015.10 - 24679550 Apr 27, 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
463553685, 200395480, ss4285496999, ss4984849820 NC_000015.10:24679549:CAGGTGGTG: NC_000015.10:24679549:CAGGTGGTGCA:…

NC_000015.10:24679549:CAGGTGGTGCA:CA

(self)
16309494509 NC_000015.10:24679549:CAGGTGGTGCA:…

NC_000015.10:24679549:CAGGTGGTGCA:CA

NC_000015.10:24679549:CAGGTGGTGCA:…

NC_000015.10:24679549:CAGGTGGTGCA:CA

(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 rs1486015780

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