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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr1:1104453-1104457 (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.

Variation Type
Indel Insertion and Deletion
delT=0.001413 (374/264690, TOPMED)
delT=0.001412 (198/140274, GnomAD)
delT=0.00085 (12/14050, ALFA) (+ 1 more)
delT=0.0010 (5/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
C1orf159 : Intron Variant
0 citations
Genomic View
See rs on genome

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.1104457del
GRCh37.p13 chr 1 NC_000001.10:g.1039837del
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+105…


N/A Intron Variant
C1orf159 transcript variant 3 NM_001363525.2:c.-136+105…


N/A Intron Variant
C1orf159 transcript variant 2 NM_017891.5:c.-136+11607d…


N/A Intron Variant

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 14050 TTTTT=0.99915 TTTT=0.00085
European Sub 9690 TTTTT=1.0000 TTTT=0.0000
African Sub 2898 TTTTT=0.9959 TTTT=0.0041
African Others Sub 114 TTTTT=1.000 TTTT=0.000
African American Sub 2784 TTTTT=0.9957 TTTT=0.0043
Asian Sub 112 TTTTT=1.000 TTTT=0.000
East Asian Sub 86 TTTTT=1.00 TTTT=0.00
Other Asian Sub 26 TTTTT=1.00 TTTT=0.00
Latin American 1 Sub 146 TTTTT=1.000 TTTT=0.000
Latin American 2 Sub 610 TTTTT=1.000 TTTT=0.000
South Asian Sub 98 TTTTT=1.00 TTTT=0.00
Other Sub 496 TTTTT=1.000 TTTT=0.000


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").

Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 (T)5=0.998587 delT=0.001413
gnomAD - Genomes Global Study-wide 140274 (T)5=0.998588 delT=0.001412
gnomAD - Genomes European Sub 75966 (T)5=1.00000 delT=0.00000
gnomAD - Genomes African Sub 42046 (T)5=0.99536 delT=0.00464
gnomAD - Genomes American Sub 13658 (T)5=0.99993 delT=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3322 (T)5=1.0000 delT=0.0000
gnomAD - Genomes East Asian Sub 3130 (T)5=1.0000 delT=0.0000
gnomAD - Genomes Other Sub 2152 (T)5=0.9991 delT=0.0009
1000Genomes Global Study-wide 5008 (T)5=0.9990 delT=0.0010
1000Genomes African Sub 1322 (T)5=0.9962 delT=0.0038
1000Genomes East Asian Sub 1008 (T)5=1.0000 delT=0.0000
1000Genomes Europe Sub 1006 (T)5=1.0000 delT=0.0000
1000Genomes South Asian Sub 978 (T)5=1.000 delT=0.000
1000Genomes American Sub 694 (T)5=1.000 delT=0.000

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 (T)5= delT
GRCh38.p13 chr 1 NC_000001.11:g.1104453_1104457= NC_000001.11:g.1104457del
GRCh37.p13 chr 1 NC_000001.10:g.1039833_1039837= NC_000001.10:g.1039837del
C1orf159 transcript variant 1 NM_001330306.2:c.-136+10569= NM_001330306.2:c.-136+10569del
C1orf159 transcript variant 3 NM_001363525.2:c.-136+10569= NM_001363525.2:c.-136+10569del
C1orf159 transcript variant 2 NM_017891.4:c.-136+11607= NM_017891.4:c.-136+11607del
C1orf159 transcript variant 2 NM_017891.5:c.-136+11607= NM_017891.5:c.-136+11607del
C1orf159 transcript variant X1 XM_005244764.1:c.-136+10569= XM_005244764.1:c.-136+10569del
C1orf159 transcript variant X16 XM_005244765.1:c.-136+11607= XM_005244765.1:c.-136+11607del
C1orf159 transcript variant X3 XM_005244766.1:c.-136+11607= XM_005244766.1:c.-136+11607del

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#.

7 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss325997326 May 09, 2011 (134)
2 LUNTER ss550899278 Apr 25, 2013 (138)
3 1000GENOMES ss1367645827 Aug 21, 2014 (142)
4 TOPMED ss2321524458 Dec 20, 2016 (150)
5 GNOMAD ss2750670424 Nov 08, 2017 (151)
6 TOPMED ss3066468955 Nov 08, 2017 (151)
7 TOPMED ss4436516300 Apr 25, 2021 (155)
8 1000Genomes NC_000001.10 - 1039833 Oct 11, 2018 (152)
9 gnomAD - Genomes NC_000001.11 - 1104453 Apr 25, 2021 (155)
10 TopMed NC_000001.11 - 1104453 Apr 25, 2021 (155)
11 ALFA NC_000001.11 - 1104453 Apr 25, 2021 (155)

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
ss325997326, ss550899278 NC_000001.9:1029695:T: NC_000001.11:1104452:TTTTT:TTTT (self)
14908, ss1367645827, ss2321524458, ss2750670424 NC_000001.10:1039832:T: NC_000001.11:1104452:TTTTT:TTTT (self)
138316, 69061, 122635, ss3066468955, ss4436516300 NC_000001.11:1104452:T: NC_000001.11:1104452:TTTTT:TTTT (self)
2392424534 NC_000001.11:1104452:TTTTT:TTTT NC_000001.11:1104452:TTTTT:TTTT (self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs149608175


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