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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.

rs141449834

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:1101488-1101489 (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
delAT
Variation Type
Deletion
Frequency
delAT=0.064818 (9084/140146, GnomAD)
delAT=0.01366 (207/15150, ALFA)
delAT=0.0464 (208/4480, Estonian) (+ 2 more)
delAT=0.027 (16/600, NorthernSweden)
delAT=0.03 (1/40, 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.1101488_1101489del
GRCh37.p13 chr 1 NC_000001.10:g.1036868_1036869del
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.-135-938…

NM_001330306.2:c.-135-9386_-135-9385del

N/A Intron Variant
C1orf159 transcript variant 3 NM_001363525.2:c.-135-938…

NM_001363525.2:c.-135-9386_-135-9385del

N/A Intron Variant
C1orf159 transcript variant 2 NM_017891.5:c.-135-9386_-…

NM_017891.5:c.-135-9386_-135-9385del

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 15150 AT=0.98634 =0.01366
European Sub 11424 AT=0.98188 =0.01812
African Sub 2294 AT=1.0000 =0.0000
African Others Sub 84 AT=1.00 =0.00
African American Sub 2210 AT=1.0000 =0.0000
Asian Sub 108 AT=1.000 =0.000
East Asian Sub 84 AT=1.00 =0.00
Other Asian Sub 24 AT=1.00 =0.00
Latin American 1 Sub 146 AT=1.000 =0.000
Latin American 2 Sub 610 AT=1.000 =0.000
South Asian Sub 94 AT=1.00 =0.00
Other Sub 474 AT=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 140146 AT=0.935182 delAT=0.064818
gnomAD - Genomes European Sub 75916 AT=0.97190 delAT=0.02810
gnomAD - Genomes African Sub 41980 AT=0.84769 delAT=0.15231
gnomAD - Genomes American Sub 13644 AT=0.97354 delAT=0.02646
gnomAD - Genomes Ashkenazi Jewish Sub 3324 AT=0.9744 delAT=0.0256
gnomAD - Genomes East Asian Sub 3130 AT=1.0000 delAT=0.0000
gnomAD - Genomes Other Sub 2152 AT=0.9484 delAT=0.0516
Genetic variation in the Estonian population Estonian Study-wide 4480 AT=0.9536 delAT=0.0464
Northern Sweden ACPOP Study-wide 600 AT=0.973 delAT=0.027
The Danish reference pan genome Danish Study-wide 40 AT=0.97 delAT=0.03
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 AT= delAT
GRCh38.p13 chr 1 NC_000001.11:g.1101488_1101489= NC_000001.11:g.1101488_1101489del
GRCh37.p13 chr 1 NC_000001.10:g.1036868_1036869= NC_000001.10:g.1036868_1036869del
C1orf159 transcript variant 1 NM_001330306.2:c.-135-9385= NM_001330306.2:c.-135-9386_-135-9385del
C1orf159 transcript variant 3 NM_001363525.2:c.-135-9385= NM_001363525.2:c.-135-9386_-135-9385del
C1orf159 transcript variant 2 NM_017891.4:c.-135-9385= NM_017891.4:c.-135-9386_-135-9385del
C1orf159 transcript variant 2 NM_017891.5:c.-135-9385= NM_017891.5:c.-135-9386_-135-9385del
C1orf159 transcript variant X1 XM_005244764.1:c.-135-9385= XM_005244764.1:c.-135-9386_-135-9385del
C1orf159 transcript variant X16 XM_005244765.1:c.-135-9385= XM_005244765.1:c.-135-9386_-135-9385del
C1orf159 transcript variant X3 XM_005244766.1:c.-135-9385= XM_005244766.1:c.-135-9386_-135-9385del
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#.

8 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss325997320 May 09, 2011 (134)
2 EVA_GENOME_DK ss1573868714 Apr 01, 2015 (144)
3 JJLAB ss2030297880 Sep 14, 2016 (149)
4 GNOMAD ss2750670132 Jan 10, 2018 (151)
5 SWEGEN ss2986154126 Jan 10, 2018 (151)
6 MCHAISSO ss3065282678 Jan 10, 2018 (151)
7 EGCUT_WGS ss3654265215 Jul 12, 2019 (153)
8 ACPOP ss3726718563 Jul 12, 2019 (153)
9 Genetic variation in the Estonian population NC_000001.10 - 1036868 Oct 11, 2018 (152)
10 The Danish reference pan genome NC_000001.10 - 1036868 Apr 25, 2020 (154)
11 gnomAD - Genomes NC_000001.11 - 1101488 Apr 25, 2021 (155)
12 Northern Sweden NC_000001.10 - 1036868 Jul 12, 2019 (153)
13 ALFA NC_000001.11 - 1101488 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
ss325997320 NC_000001.9:1026730:AT: NC_000001.11:1101487:AT: (self)
3463, 120346, 3428, ss1573868714, ss2030297880, ss2750670132, ss2986154126, ss3654265215, ss3726718563 NC_000001.10:1036867:AT: NC_000001.11:1101487:AT: (self)
137562, 4183637790, ss3065282678 NC_000001.11:1101487:AT: NC_000001.11:1101487:AT: (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 rs141449834

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