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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.

rs139568537

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1085503 (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
delA
Variation Type
Deletion
Frequency
delA=0.032353 (4513/139492, GnomAD)
delA=0.00000 (0/11244, ALFA)
delA=0.0292 (146/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
C1orf159 : 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.1085503del
GRCh37.p13 chr 1 NC_000001.10:g.1020883del
Gene: C1orf159, chromosome 1 open reading frame 159 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
C1orf159 transcript variant 1 NM_001330306.2:c.553+375d…

NM_001330306.2:c.553+375del

N/A Intron Variant
C1orf159 transcript variant 3 NM_001363525.2:c.445+375d…

NM_001363525.2:c.445+375del

N/A Intron Variant
C1orf159 transcript variant 2 NM_017891.5:c.445+375del 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

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 11244 A=1.00000 =0.00000
European Sub 7600 A=1.0000 =0.0000
African Sub 2260 A=1.0000 =0.0000
African Others Sub 82 A=1.00 =0.00
African American Sub 2178 A=1.0000 =0.0000
Asian Sub 108 A=1.000 =0.000
East Asian Sub 84 A=1.00 =0.00
Other Asian Sub 24 A=1.00 =0.00
Latin American 1 Sub 128 A=1.000 =0.000
Latin American 2 Sub 606 A=1.000 =0.000
South Asian Sub 94 A=1.00 =0.00
Other Sub 448 A=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
gnomAD - Genomes Global Study-wide 139492 A=0.967647 delA=0.032353
gnomAD - Genomes European Sub 75562 A=0.99877 delA=0.00123
gnomAD - Genomes African Sub 41828 A=0.90066 delA=0.09934
gnomAD - Genomes American Sub 13540 A=0.98575 delA=0.01425
gnomAD - Genomes Ashkenazi Jewish Sub 3312 A=0.9979 delA=0.0021
gnomAD - Genomes East Asian Sub 3104 A=1.0000 delA=0.0000
gnomAD - Genomes Other Sub 2146 A=0.9697 delA=0.0303
Allele Frequency Aggregator Total Global 11244 A=1.00000 delA=0.00000
Allele Frequency Aggregator European Sub 7600 A=1.0000 delA=0.0000
Allele Frequency Aggregator African Sub 2260 A=1.0000 delA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 606 A=1.000 delA=0.000
Allele Frequency Aggregator Other Sub 448 A=1.000 delA=0.000
Allele Frequency Aggregator Latin American 1 Sub 128 A=1.000 delA=0.000
Allele Frequency Aggregator Asian Sub 108 A=1.000 delA=0.000
Allele Frequency Aggregator South Asian Sub 94 A=1.00 delA=0.00
1000Genomes Global Study-wide 5008 A=0.9708 delA=0.0292
1000Genomes African Sub 1322 A=0.8986 delA=0.1014
1000Genomes East Asian Sub 1008 A=1.0000 delA=0.0000
1000Genomes Europe Sub 1006 A=0.9990 delA=0.0010
1000Genomes South Asian Sub 978 A=1.000 delA=0.000
1000Genomes American Sub 694 A=0.984 delA=0.016
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 A= delA
GRCh38.p13 chr 1 NC_000001.11:g.1085503= NC_000001.11:g.1085503del
GRCh37.p13 chr 1 NC_000001.10:g.1020883= NC_000001.10:g.1020883del
C1orf159 transcript variant 1 NM_001330306.2:c.553+375= NM_001330306.2:c.553+375del
C1orf159 transcript variant 3 NM_001363525.2:c.445+375= NM_001363525.2:c.445+375del
C1orf159 transcript variant 2 NM_017891.4:c.445+375= NM_017891.4:c.445+375del
C1orf159 transcript variant 2 NM_017891.5:c.445+375= NM_017891.5:c.445+375del
C1orf159 transcript variant X1 XM_005244764.1:c.553+375= XM_005244764.1:c.553+375del
C1orf159 transcript variant X16 XM_005244765.1:c.445+375= XM_005244765.1:c.445+375del
C1orf159 transcript variant X3 XM_005244766.1:c.553+375= XM_005244766.1:c.553+375del
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, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss325997314 May 09, 2011 (134)
2 1000GENOMES ss498763981 May 04, 2012 (137)
3 LUNTER ss550899272 Apr 25, 2013 (138)
4 TISHKOFF ss553708593 Apr 25, 2013 (138)
5 1000GENOMES ss1367645804 Aug 21, 2014 (142)
6 JJLAB ss2030297872 Sep 14, 2016 (149)
7 GNOMAD ss2750668314 Nov 08, 2017 (151)
8 TOPMED ss3066464484 Nov 08, 2017 (151)
9 KHV_HUMAN_GENOMES ss3798746559 Jul 12, 2019 (153)
10 1000Genomes NC_000001.10 - 1020883 Oct 11, 2018 (152)
11 gnomAD - Genomes NC_000001.11 - 1085503 Apr 25, 2021 (155)
12 ALFA NC_000001.11 - 1085503 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
ss325997314, ss550899272 NC_000001.9:1010745:A: NC_000001.11:1085502:A: (self)
14166, ss498763981, ss553708593, ss1367645804, ss2030297872, ss2750668314 NC_000001.10:1020882:A: NC_000001.11:1085502:A: (self)
133489, 1364991849, ss3066464484, ss3798746559 NC_000001.11:1085502:A: NC_000001.11:1085502: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 rs139568537

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