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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.

rs71576598

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1103618-1103624 (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
delTCC
Variation Type
Indel Insertion and Deletion
Frequency
delTCC=0.255669 (67673/264690, TOPMED)
delTCC=0.243791 (33885/138992, GnomAD)
delTCC=0.19800 (3667/18520, ALFA) (+ 10 more)
delTCC=0.20656 (3462/16760, 8.3KJPN)
delTCC=0.2827 (1416/5008, 1000G)
delTCC=0.1304 (584/4480, Estonian)
delTCC=0.1261 (486/3854, ALSPAC)
delTCC=0.1402 (520/3708, TWINSUK)
delTCC=0.2298 (421/1832, Korea1K)
delTCC=0.124 (124/998, GoNL)
delTCC=0.130 (78/600, NorthernSweden)
delTCC=0.144 (31/216, Vietnamese)
delTCC=0.15 (6/40, GENOME_DK)
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.1103619TCC[1]
GRCh37.p13 chr 1 NC_000001.10:g.1038999TCC[1]
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+114…

NM_001330306.2:c.-136+11402_-136+11404del

N/A Intron Variant
C1orf159 transcript variant 3 NM_001363525.2:c.-136+114…

NM_001363525.2:c.-136+11402_-136+11404del

N/A Intron Variant
C1orf159 transcript variant 2 NM_017891.5:c.-135-11517_…

NM_017891.5:c.-135-11517_-135-11515del

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 CTCCTCC=0.80200 CTCC=0.19800
European Sub 14152 CTCCTCC=0.86016 CTCC=0.13984
African Sub 2898 CTCCTCC=0.5293 CTCC=0.4707
African Others Sub 114 CTCCTCC=0.430 CTCC=0.570
African American Sub 2784 CTCCTCC=0.5334 CTCC=0.4666
Asian Sub 112 CTCCTCC=0.821 CTCC=0.179
East Asian Sub 86 CTCCTCC=0.86 CTCC=0.14
Other Asian Sub 26 CTCCTCC=0.69 CTCC=0.31
Latin American 1 Sub 146 CTCCTCC=0.719 CTCC=0.281
Latin American 2 Sub 610 CTCCTCC=0.821 CTCC=0.179
South Asian Sub 98 CTCCTCC=0.85 CTCC=0.15
Other Sub 504 CTCCTCC=0.724 CTCC=0.276


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 (CTC)2C=0.744331 delTCC=0.255669
gnomAD - Genomes Global Study-wide 138992 (CTC)2C=0.756209 delTCC=0.243791
gnomAD - Genomes European Sub 75312 (CTC)2C=0.86349 delTCC=0.13651
gnomAD - Genomes African Sub 41634 (CTC)2C=0.54047 delTCC=0.45953
gnomAD - Genomes American Sub 13520 (CTC)2C=0.80703 delTCC=0.19297
gnomAD - Genomes Ashkenazi Jewish Sub 3304 (CTC)2C=0.7948 delTCC=0.2052
gnomAD - Genomes East Asian Sub 3086 (CTC)2C=0.7881 delTCC=0.2119
gnomAD - Genomes Other Sub 2136 (CTC)2C=0.7514 delTCC=0.2486
Allele Frequency Aggregator Total Global 18520 (CTC)2C=0.80200 delTCC=0.19800
Allele Frequency Aggregator European Sub 14152 (CTC)2C=0.86016 delTCC=0.13984
Allele Frequency Aggregator African Sub 2898 (CTC)2C=0.5293 delTCC=0.4707
Allele Frequency Aggregator Latin American 2 Sub 610 (CTC)2C=0.821 delTCC=0.179
Allele Frequency Aggregator Other Sub 504 (CTC)2C=0.724 delTCC=0.276
Allele Frequency Aggregator Latin American 1 Sub 146 (CTC)2C=0.719 delTCC=0.281
Allele Frequency Aggregator Asian Sub 112 (CTC)2C=0.821 delTCC=0.179
Allele Frequency Aggregator South Asian Sub 98 (CTC)2C=0.85 delTCC=0.15
8.3KJPN JAPANESE Study-wide 16760 (CTC)2C=0.79344 delTCC=0.20656
1000Genomes Global Study-wide 5008 (CTC)2C=0.7173 delTCC=0.2827
1000Genomes African Sub 1322 (CTC)2C=0.4637 delTCC=0.5363
1000Genomes East Asian Sub 1008 (CTC)2C=0.7798 delTCC=0.2202
1000Genomes Europe Sub 1006 (CTC)2C=0.8658 delTCC=0.1342
1000Genomes South Asian Sub 978 (CTC)2C=0.764 delTCC=0.236
1000Genomes American Sub 694 (CTC)2C=0.829 delTCC=0.171
Genetic variation in the Estonian population Estonian Study-wide 4480 (CTC)2C=0.8696 delTCC=0.1304
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 (CTC)2C=0.8739 delTCC=0.1261
UK 10K study - Twins TWIN COHORT Study-wide 3708 (CTC)2C=0.8598 delTCC=0.1402
Korean Genome Project KOREAN Study-wide 1832 (CTC)2C=0.7702 delTCC=0.2298
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 (CTC)2C=0.876 delTCC=0.124
Northern Sweden ACPOP Study-wide 600 (CTC)2C=0.870 delTCC=0.130
A Vietnamese Genetic Variation Database Global Study-wide 216 (CTC)2C=0.856 delTCC=0.144
The Danish reference pan genome Danish Study-wide 40 (CTC)2C=0.85 delTCC=0.15
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 (CTC)2C= delTCC
GRCh38.p13 chr 1 NC_000001.11:g.1103618_1103624= NC_000001.11:g.1103619TCC[1]
GRCh37.p13 chr 1 NC_000001.10:g.1038998_1039004= NC_000001.10:g.1038999TCC[1]
C1orf159 transcript variant 1 NM_001330306.2:c.-136+11404= NM_001330306.2:c.-136+11402_-136+11404del
C1orf159 transcript variant 3 NM_001363525.2:c.-136+11404= NM_001363525.2:c.-136+11402_-136+11404del
C1orf159 transcript variant 2 NM_017891.4:c.-135-11515= NM_017891.4:c.-135-11517_-135-11515del
C1orf159 transcript variant 2 NM_017891.5:c.-135-11515= NM_017891.5:c.-135-11517_-135-11515del
C1orf159 transcript variant X1 XM_005244764.1:c.-136+11404= XM_005244764.1:c.-136+11402_-136+11404del
C1orf159 transcript variant X16 XM_005244765.1:c.-135-11515= XM_005244765.1:c.-135-11517_-135-11515del
C1orf159 transcript variant X3 XM_005244766.1:c.-135-11515= XM_005244766.1:c.-135-11517_-135-11515del
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#.

42 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 HGSV ss81753870 Aug 21, 2014 (142)
2 HGSV ss81999157 Aug 21, 2014 (142)
3 HUMANGENOME_JCVI ss98565696 Feb 13, 2009 (130)
4 BUSHMAN ss193082083 Jul 04, 2010 (132)
5 GMI ss287939664 May 04, 2012 (137)
6 PJP ss294562410 May 09, 2011 (135)
7 PJP ss294562411 Aug 21, 2014 (142)
8 1000GENOMES ss325997187 May 09, 2011 (135)
9 1000GENOMES ss325997323 May 09, 2011 (135)
10 1000GENOMES ss325997759 May 09, 2011 (135)
11 1000GENOMES ss498763988 May 04, 2012 (137)
12 LUNTER ss550899276 Apr 25, 2013 (138)
13 LUNTER ss550903262 Apr 25, 2013 (138)
14 LUNTER ss552739239 Apr 25, 2013 (138)
15 TISHKOFF ss553708596 Apr 25, 2013 (138)
16 SSMP ss663105525 Apr 01, 2015 (144)
17 EVA-GONL ss974771853 Aug 21, 2014 (142)
18 1000GENOMES ss1367645825 Aug 21, 2014 (142)
19 DDI ss1536213981 Apr 01, 2015 (144)
20 EVA_GENOME_DK ss1573868717 Apr 01, 2015 (144)
21 EVA_DECODE ss1584131784 Apr 01, 2015 (144)
22 EVA_UK10K_ALSPAC ss1700146174 Apr 01, 2015 (144)
23 EVA_UK10K_TWINSUK ss1700154939 Apr 01, 2015 (144)
24 HAMMER_LAB ss1793716719 Sep 08, 2015 (146)
25 JJLAB ss2030297881 Sep 14, 2016 (149)
26 TOPMED ss2321524394 Dec 20, 2016 (150)
27 SYSTEMSBIOZJU ss2624265489 Nov 08, 2017 (151)
28 GNOMAD ss2750670358 Nov 08, 2017 (151)
29 SWEGEN ss2986154161 Nov 08, 2017 (151)
30 MCHAISSO ss3064386204 Nov 08, 2017 (151)
31 MCHAISSO ss3065282681 Nov 08, 2017 (151)
32 TOPMED ss3066468772 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3645022508 Oct 11, 2018 (152)
34 URBANLAB ss3646581883 Oct 11, 2018 (152)
35 EGCUT_WGS ss3654265243 Jul 12, 2019 (153)
36 EVA_DECODE ss3685997706 Jul 12, 2019 (153)
37 ACPOP ss3726718580 Jul 12, 2019 (153)
38 KHV_HUMAN_GENOMES ss3798746744 Jul 12, 2019 (153)
39 EVA ss3825982547 Apr 25, 2020 (154)
40 KOGIC ss3943635962 Apr 25, 2020 (154)
41 TOPMED ss4436516071 Apr 25, 2021 (155)
42 TOMMO_GENOMICS ss5142066236 Apr 25, 2021 (155)
43 1000Genomes NC_000001.10 - 1038998 Oct 11, 2018 (152)
44 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 1038998 Oct 11, 2018 (152)
45 Genetic variation in the Estonian population NC_000001.10 - 1038998 Oct 11, 2018 (152)
46 The Danish reference pan genome NC_000001.10 - 1038998 Apr 25, 2020 (154)
47 gnomAD - Genomes NC_000001.11 - 1103618 Apr 25, 2021 (155)
48 Genome of the Netherlands Release 5 NC_000001.10 - 1038998 Apr 25, 2020 (154)
49 Korean Genome Project NC_000001.11 - 1103618 Apr 25, 2020 (154)
50 Northern Sweden NC_000001.10 - 1038998 Jul 12, 2019 (153)
51 8.3KJPN NC_000001.10 - 1038998 Apr 25, 2021 (155)
52 TopMed NC_000001.11 - 1103618 Apr 25, 2021 (155)
53 UK 10K study - Twins NC_000001.10 - 1038998 Oct 11, 2018 (152)
54 A Vietnamese Genetic Variation Database NC_000001.10 - 1038998 Jul 12, 2019 (153)
55 ALFA NC_000001.11 - 1103618 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)
rs57167918 May 23, 2008 (130)
rs147192355 Sep 17, 2011 (135)
rs149207793 Sep 17, 2011 (135)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss81753870, ss81999157 NC_000001.8:1078924:TCC: NC_000001.11:1103617:CTCCTCC:CTCC (self)
ss287939664, ss294562410, ss325997187, ss325997323, ss325997759, ss550899276, ss550903262, ss552739239, ss1584131784 NC_000001.9:1028860:CTC: NC_000001.11:1103617:CTCCTCC:CTCC (self)
ss294562411 NC_000001.9:1028864:TCC: NC_000001.11:1103617:CTCCTCC:CTCC (self)
14879, 4692, 3491, 120348, 2189, 3445, 35543, 4692, 1052, ss498763988, ss663105525, ss974771853, ss1367645825, ss1536213981, ss1573868717, ss1700146174, ss1700154939, ss1793716719, ss2030297881, ss2321524394, ss2624265489, ss2750670358, ss2986154161, ss3654265243, ss3726718580, ss3825982547, ss5142066236 NC_000001.10:1038997:CTC: NC_000001.11:1103617:CTCCTCC:CTCC (self)
ss553708596 NC_000001.10:1039001:TCC: NC_000001.11:1103617:CTCCTCC:CTCC (self)
138130, 13963, 68911, 122406, ss3064386204, ss3065282681, ss3066468772, ss3645022508, ss3646581883, ss3685997706, ss3798746744, ss3943635962, ss4436516071 NC_000001.11:1103617:CTC: NC_000001.11:1103617:CTCCTCC:CTCC (self)
684006112 NC_000001.11:1103617:CTCCTCC:CTCC NC_000001.11:1103617:CTCCTCC:CTCC (self)
ss98565696 NT_004350.19:517629:CTC: NC_000001.11:1103617:CTCCTCC:CTCC (self)
ss193082083 NT_032977.10:517629:CTC: NC_000001.11:1103617:CTCCTCC:CTCC (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 rs71576598

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