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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.

rs2037707603

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr21:25891680-25891681 (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
delGT
Variation Type
Deletion
Frequency
delGT=0.000004 (1/264690, TOPMED)
delGT=0.000007 (1/140270, GnomAD)
delGT=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
APP : 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 21 NC_000021.9:g.25891680_25891681del
GRCh37.p13 chr 21 NC_000021.8:g.27263992_27263993del
APP RefSeqGene NG_007376.2:g.284448_284449del
Gene: APP, amyloid beta precursor protein (minus strand)
Molecule type Change Amino acid[Codon] SO Term
APP transcript variant 1 NM_000484.4:c.2211+41_221…

NM_000484.4:c.2211+41_2211+42del

N/A Intron Variant
APP transcript variant 4 NM_001136016.3:c.2139+41_…

NM_001136016.3:c.2139+41_2139+42del

N/A Intron Variant
APP transcript variant 5 NM_001136129.3:c.1818+41_…

NM_001136129.3:c.1818+41_1818+42del

N/A Intron Variant
APP transcript variant 6 NM_001136130.3:c.2043+41_…

NM_001136130.3:c.2043+41_2043+42del

N/A Intron Variant
APP transcript variant 7 NM_001136131.3:c.1881+41_…

NM_001136131.3:c.1881+41_1881+42del

N/A Intron Variant
APP transcript variant 8 NM_001204301.2:c.2157+41_…

NM_001204301.2:c.2157+41_2157+42del

N/A Intron Variant
APP transcript variant 9 NM_001204302.2:c.2100+41_…

NM_001204302.2:c.2100+41_2100+42del

N/A Intron Variant
APP transcript variant 10 NM_001204303.2:c.1932+41_…

NM_001204303.2:c.1932+41_1932+42del

N/A Intron Variant
APP transcript variant 11 NM_001385253.1:c.2043+41_…

NM_001385253.1:c.2043+41_2043+42del

N/A Intron Variant
APP transcript variant 2 NM_201413.3:c.2154+41_215…

NM_201413.3:c.2154+41_2154+42del

N/A Intron Variant
APP transcript variant 3 NM_201414.3:c.1986+41_198…

NM_201414.3:c.1986+41_1986+42del

N/A Intron Variant
APP transcript variant X1 XM_024452075.1: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

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 10680 GT=1.00000 =0.00000
European Sub 6962 GT=1.0000 =0.0000
African Sub 2294 GT=1.0000 =0.0000
African Others Sub 84 GT=1.00 =0.00
African American Sub 2210 GT=1.0000 =0.0000
Asian Sub 108 GT=1.000 =0.000
East Asian Sub 84 GT=1.00 =0.00
Other Asian Sub 24 GT=1.00 =0.00
Latin American 1 Sub 146 GT=1.000 =0.000
Latin American 2 Sub 610 GT=1.000 =0.000
South Asian Sub 94 GT=1.00 =0.00
Other Sub 466 GT=1.000 =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 GT=0.999996 delGT=0.000004
gnomAD - Genomes Global Study-wide 140270 GT=0.999993 delGT=0.000007
gnomAD - Genomes European Sub 75952 GT=0.99999 delGT=0.00001
gnomAD - Genomes African Sub 42046 GT=1.00000 delGT=0.00000
gnomAD - Genomes American Sub 13664 GT=1.00000 delGT=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 GT=1.0000 delGT=0.0000
gnomAD - Genomes East Asian Sub 3132 GT=1.0000 delGT=0.0000
gnomAD - Genomes Other Sub 2152 GT=1.0000 delGT=0.0000
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 GT= delGT
GRCh38.p13 chr 21 NC_000021.9:g.25891680_25891681= NC_000021.9:g.25891680_25891681del
GRCh37.p13 chr 21 NC_000021.8:g.27263992_27263993= NC_000021.8:g.27263992_27263993del
APP RefSeqGene NG_007376.2:g.284448_284449= NG_007376.2:g.284448_284449del
APP transcript variant 1 NM_000484.3:c.2211+42= NM_000484.3:c.2211+41_2211+42del
APP transcript variant 1 NM_000484.4:c.2211+42= NM_000484.4:c.2211+41_2211+42del
APP transcript variant 4 NM_001136016.3:c.2139+42= NM_001136016.3:c.2139+41_2139+42del
APP transcript variant 5 NM_001136129.2:c.1818+42= NM_001136129.2:c.1818+41_1818+42del
APP transcript variant 5 NM_001136129.3:c.1818+42= NM_001136129.3:c.1818+41_1818+42del
APP transcript variant 6 NM_001136130.2:c.2043+42= NM_001136130.2:c.2043+41_2043+42del
APP transcript variant 6 NM_001136130.3:c.2043+42= NM_001136130.3:c.2043+41_2043+42del
APP transcript variant 7 NM_001136131.2:c.1881+42= NM_001136131.2:c.1881+41_1881+42del
APP transcript variant 7 NM_001136131.3:c.1881+42= NM_001136131.3:c.1881+41_1881+42del
APP transcript variant 8 NM_001204301.1:c.2157+42= NM_001204301.1:c.2157+41_2157+42del
APP transcript variant 8 NM_001204301.2:c.2157+42= NM_001204301.2:c.2157+41_2157+42del
APP transcript variant 9 NM_001204302.1:c.2100+42= NM_001204302.1:c.2100+41_2100+42del
APP transcript variant 9 NM_001204302.2:c.2100+42= NM_001204302.2:c.2100+41_2100+42del
APP transcript variant 10 NM_001204303.1:c.1932+42= NM_001204303.1:c.1932+41_1932+42del
APP transcript variant 10 NM_001204303.2:c.1932+42= NM_001204303.2:c.1932+41_1932+42del
APP transcript variant 11 NM_001385253.1:c.2043+42= NM_001385253.1:c.2043+41_2043+42del
APP transcript variant 2 NM_201413.2:c.2154+42= NM_201413.2:c.2154+41_2154+42del
APP transcript variant 2 NM_201413.3:c.2154+42= NM_201413.3:c.2154+41_2154+42del
APP transcript variant 3 NM_201414.2:c.1986+42= NM_201414.2:c.1986+41_1986+42del
APP transcript variant 3 NM_201414.3:c.1986+42= NM_201414.3:c.1986+41_1986+42del
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 ss4358885962 Apr 26, 2021 (155)
2 TOPMED ss5098677818 Apr 26, 2021 (155)
3 gnomAD - Genomes NC_000021.9 - 25891680 Apr 26, 2021 (155)
4 TopMed NC_000021.9 - 25891680 Apr 26, 2021 (155)
5 ALFA NC_000021.9 - 25891680 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
560793144, 373786764, 2494068703, ss4358885962, ss5098677818 NC_000021.9:25891679:GT: NC_000021.9:25891679:GT:
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 rs2037707603

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