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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.

rs142862168

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1114778-1114779 (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
delC
Variation Type
Indel Insertion and Deletion
Frequency
delC=0.007443 (1970/264690, TOPMED)
delC=0.007516 (1046/139172, GnomAD)
delC=0.00475 (88/18520, ALFA) (+ 3 more)
delC=0.0082 (41/5008, 1000G)
delC=0.0004 (2/4480, Estonian)
delC=0.002 (2/998, GoNL)
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.1114779del
GRCh37.p13 chr 1 NC_000001.10:g.1050159del
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.-136+244…

NM_001330306.2:c.-136+244del

N/A Intron Variant
C1orf159 transcript variant 3 NM_001363525.2:c.-136+244…

NM_001363525.2:c.-136+244del

N/A Intron Variant
C1orf159 transcript variant 2 NM_017891.5:c.-136+1282del 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 18520 CC=0.99525 C=0.00475
European Sub 14152 CC=0.99873 C=0.00127
African Sub 2898 CC=0.9786 C=0.0214
African Others Sub 114 CC=0.991 C=0.009
African American Sub 2784 CC=0.9781 C=0.0219
Asian Sub 112 CC=1.000 C=0.000
East Asian Sub 86 CC=1.00 C=0.00
Other Asian Sub 26 CC=1.00 C=0.00
Latin American 1 Sub 146 CC=0.986 C=0.014
Latin American 2 Sub 610 CC=0.998 C=0.002
South Asian Sub 98 CC=1.00 C=0.00
Other Sub 504 CC=0.990 C=0.010


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 CC=0.992557 delC=0.007443
gnomAD - Genomes Global Study-wide 139172 CC=0.992484 delC=0.007516
gnomAD - Genomes European Sub 75202 CC=0.99903 delC=0.00097
gnomAD - Genomes African Sub 41820 CC=0.97836 delC=0.02164
gnomAD - Genomes American Sub 13592 CC=0.99654 delC=0.00346
gnomAD - Genomes Ashkenazi Jewish Sub 3302 CC=0.9985 delC=0.0015
gnomAD - Genomes East Asian Sub 3118 CC=1.0000 delC=0.0000
gnomAD - Genomes Other Sub 2138 CC=0.9925 delC=0.0075
1000Genomes Global Study-wide 5008 CC=0.9918 delC=0.0082
1000Genomes African Sub 1322 CC=0.9697 delC=0.0303
1000Genomes East Asian Sub 1008 CC=1.0000 delC=0.0000
1000Genomes Europe Sub 1006 CC=1.0000 delC=0.0000
1000Genomes South Asian Sub 978 CC=1.000 delC=0.000
1000Genomes American Sub 694 CC=0.999 delC=0.001
Genetic variation in the Estonian population Estonian Study-wide 4480 CC=0.9996 delC=0.0004
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 CC=0.998 delC=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 CC= delC
GRCh38.p13 chr 1 NC_000001.11:g.1114778_1114779= NC_000001.11:g.1114779del
GRCh37.p13 chr 1 NC_000001.10:g.1050158_1050159= NC_000001.10:g.1050159del
C1orf159 transcript variant 1 NM_001330306.2:c.-136+244= NM_001330306.2:c.-136+244del
C1orf159 transcript variant 3 NM_001363525.2:c.-136+244= NM_001363525.2:c.-136+244del
C1orf159 transcript variant 2 NM_017891.4:c.-136+1282= NM_017891.4:c.-136+1282del
C1orf159 transcript variant 2 NM_017891.5:c.-136+1282= NM_017891.5:c.-136+1282del
C1orf159 transcript variant X1 XM_005244764.1:c.-136+244= XM_005244764.1:c.-136+244del
C1orf159 transcript variant X16 XM_005244765.1:c.-136+1282= XM_005244765.1:c.-136+1282del
C1orf159 transcript variant X3 XM_005244766.1:c.-136+1282= XM_005244766.1:c.-136+1282del
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#.

11 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss325997332 May 09, 2011 (134)
2 1000GENOMES ss498763993 May 04, 2012 (137)
3 LUNTER ss550899283 Apr 25, 2013 (138)
4 TISHKOFF ss553708598 Apr 25, 2013 (138)
5 EVA-GONL ss974771973 Aug 21, 2014 (144)
6 1000GENOMES ss1367645839 Aug 21, 2014 (144)
7 TOPMED ss2321525259 Dec 20, 2016 (150)
8 GNOMAD ss2750671560 Nov 08, 2017 (151)
9 TOPMED ss3066471378 Nov 08, 2017 (151)
10 EGCUT_WGS ss3654265416 Jul 12, 2019 (153)
11 TOPMED ss4436519104 Apr 25, 2021 (155)
12 1000Genomes NC_000001.10 - 1050158 Oct 11, 2018 (152)
13 Genetic variation in the Estonian population NC_000001.10 - 1050158 Oct 11, 2018 (152)
14 gnomAD - Genomes NC_000001.11 - 1114778 Apr 25, 2021 (155)
15 Genome of the Netherlands Release 5 NC_000001.10 - 1050158 Apr 25, 2020 (154)
16 TopMed NC_000001.11 - 1114778 Apr 25, 2021 (155)
17 ALFA NC_000001.11 - 1114778 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).

Associated ID History Updated (Build)
rs376362642 May 15, 2013 (138)
rs575694424 Apr 01, 2015 (144)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss325997332, ss550899283 NC_000001.9:1040020:C: NC_000001.11:1114777:CC:C (self)
15333, 3664, 2307, ss498763993, ss974771973, ss1367645839, ss2321525259, ss2750671560, ss3654265416 NC_000001.10:1050157:C: NC_000001.11:1114777:CC:C (self)
ss553708598 NC_000001.10:1050158:C: NC_000001.11:1114777:CC:C (self)
140988, 70842, 125439, ss3066471378, ss4436519104 NC_000001.11:1114777:C: NC_000001.11:1114777:CC:C (self)
7103722068 NC_000001.11:1114777:CC:C NC_000001.11:1114777:CC:C (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 rs142862168

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