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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 Aliases 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.

rs143496694

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr13:27254930-27254932 (GRCh38.p12) 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
dupT
Variation Type
Indel Insertion and Deletion
Frequency
dupT=0.01724 (2165/125568, TOPMED)
dupT=0.0159 (500/31396, GnomAD)
dupT=0.015 (75/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
RPL21 : Intron Variant
SNORA27 : 2KB Upstream Variant
SNORD102 : 2KB Upstream 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.p12 chr 13 NC_000013.11:g.27254932dup
GRCh37.p13 chr 13 NC_000013.10:g.27829069dup
RPL21 RefSeqGene NG_046927.1:g.8378dup
Gene: RPL21, ribosomal protein L21 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
RPL21 transcript NM_000982.3:c. N/A Intron Variant
Gene: SNORD102, small nucleolar RNA, C/D box 102 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORD102 transcript NR_002574.1:n. N/A Upstream Transcript Variant
Gene: SNORA27, small nucleolar RNA, H/ACA box 27 (plus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
SNORA27 transcript NR_002575.1:n. N/A Upstream Transcript 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
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 125568 -

No frequency provided

dupT=0.01724
gnomAD - Genomes Global Study-wide 31396 -

No frequency provided

dupT=0.0159
gnomAD - Genomes European Sub 18900 -

No frequency provided

dupT=0.0001
gnomAD - Genomes African Sub 8712 -

No frequency provided

dupT=0.056
gnomAD - Genomes East Asian Sub 1560 -

No frequency provided

dupT=0.000
gnomAD - Genomes Other Sub 1086 -

No frequency provided

dupT=0.004
gnomAD - Genomes American Sub 848 -

No frequency provided

dupT=0.01
gnomAD - Genomes Ashkenazi Jewish Sub 290 -

No frequency provided

dupT=0.00
1000Genomes Global Study-wide 5008 -

No frequency provided

dupT=0.015
1000Genomes African Sub 1322 -

No frequency provided

dupT=0.053
1000Genomes East Asian Sub 1008 -

No frequency provided

dupT=0.000
1000Genomes Europe Sub 1006 -

No frequency provided

dupT=0.000
1000Genomes South Asian Sub 978 -

No frequency provided

dupT=0.00
1000Genomes American Sub 694 -

No frequency provided

dupT=0.01
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 TTT= dupT Note
GRCh38.p12 chr 13 NC_000013.11:g.27254930...

NC_000013.11:g.27254930_27254932=

NC_000013.11:g.27254932dup
GRCh37.p13 chr 13 NC_000013.10:g.27829067...

NC_000013.10:g.27829067_27829069=

NC_000013.10:g.27829069dup
RPL21 RefSeqGene NG_046927.1:g.8376_8378= NG_046927.1:g.8378dup
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, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss328056217 May 09, 2011 (134)
2 1000GENOMES ss499932069 May 04, 2012 (137)
3 LUNTER ss552578556 Apr 25, 2013 (138)
4 TISHKOFF ss563016433 Apr 25, 2013 (138)
5 WARNICH_LAB ss678392583 Apr 25, 2013 (138)
6 1000GENOMES ss1372947014 Aug 21, 2014 (142)
7 HAMMER_LAB ss1807536525 Sep 08, 2015 (146)
8 TOPMED ss2359120720 Dec 20, 2016 (150)
9 GNOMAD ss2917832609 Nov 08, 2017 (151)
10 TOPMED ss3188526091 Nov 08, 2017 (151)
11 KHV_HUMAN_GENOMES ss3816594223 Jul 13, 2019 (153)
12 1000Genomes NC_000013.10 - 27829067 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000013.10 - 27829067 Jul 13, 2019 (153)
14 TopMed NC_000013.11 - 27254930 Oct 12, 2018 (152)
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)
rs372651082 May 15, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss328056217, ss552578556 NC_000013.9:26727066::T NC_000013.11:27254929:TTT:TTTT (self)
60426786, 164945717, ss499932069, ss678392583, ss1372947014, ss1807536525, ss2359120720, ss2917832609 NC_000013.10:27829066::T NC_000013.11:27254929:TTT:TTTT (self)
ss563016433 NC_000013.10:27829069::T NC_000013.11:27254929:TTT:TTTT (self)
97676959, ss3188526091, ss3816594223 NC_000013.11:27254929::T NC_000013.11:27254929:TTT:TTTT (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 rs143496694

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.post308+0fe9b3b