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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.

rs199745078

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:286173 (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
insCT
Variation Type
Indel Insertion and Deletion
Frequency
insCT=0.22832 (3738/16372, 8.3KJPN)
insCT=0.13058 (2129/16304, ALFA)
insCT=0.1386 (694/5008, 1000G) (+ 3 more)
insCT=0.2731 (485/1776, Korea1K)
insCT=0.156 (93/596, NorthernSweden)
insCT=0.18 (7/38, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
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.286173_286174insCT
GRCh37.p13 chr 1 NC_000001.10:g.255924_255925insCT
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 16304 T=0.86942 TCT=0.13058
European Sub 12052 T=0.86235 TCT=0.13765
African Sub 2816 T=0.8825 TCT=0.1175
African Others Sub 108 T=0.898 TCT=0.102
African American Sub 2708 T=0.8818 TCT=0.1182
Asian Sub 108 T=0.806 TCT=0.194
East Asian Sub 84 T=0.79 TCT=0.21
Other Asian Sub 24 T=0.88 TCT=0.12
Latin American 1 Sub 146 T=0.932 TCT=0.068
Latin American 2 Sub 610 T=0.913 TCT=0.087
South Asian Sub 94 T=0.90 TCT=0.10
Other Sub 478 T=0.904 TCT=0.096


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
8.3KJPN JAPANESE Study-wide 16372 -

No frequency provided

insCT=0.22832
1000Genomes Global Study-wide 5008 -

No frequency provided

insCT=0.1386
1000Genomes African Sub 1322 -

No frequency provided

insCT=0.1203
1000Genomes East Asian Sub 1008 -

No frequency provided

insCT=0.2341
1000Genomes Europe Sub 1006 -

No frequency provided

insCT=0.1292
1000Genomes South Asian Sub 978 -

No frequency provided

insCT=0.119
1000Genomes American Sub 694 -

No frequency provided

insCT=0.076
Korean Genome Project KOREAN Study-wide 1776 -

No frequency provided

insCT=0.2731
Northern Sweden ACPOP Study-wide 596 -

No frequency provided

insCT=0.156
The Danish reference pan genome Danish Study-wide 38 -

No frequency provided

insCT=0.18
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 T= insCT
GRCh38.p13 chr 1 NC_000001.11:g.286173= NC_000001.11:g.286173_286174insCT
GRCh37.p13 chr 1 NC_000001.10:g.255924= NC_000001.10:g.255924_255925insCT
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#.

17 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 GMI ss287939226 May 04, 2012 (137)
2 1000GENOMES ss498763778 May 04, 2012 (137)
3 LUNTER ss550903097 Apr 25, 2013 (138)
4 1000GENOMES ss1367645251 Aug 21, 2014 (142)
5 EVA_GENOME_DK ss1573867295 Apr 01, 2015 (144)
6 JJLAB ss2030297686 Sep 14, 2016 (149)
7 SWEGEN ss2986144547 Nov 08, 2017 (151)
8 MCHAISSO ss3063573450 Nov 08, 2017 (151)
9 MCHAISSO ss3064385964 Nov 08, 2017 (151)
10 MCHAISSO ss3065282439 Nov 08, 2017 (151)
11 TOPMED ss3066352004 Nov 08, 2017 (151)
12 URBANLAB ss3646580825 Oct 11, 2018 (152)
13 EVA_DECODE ss3685991103 Jul 12, 2019 (153)
14 ACPOP ss3726715552 Jul 12, 2019 (153)
15 KHV_HUMAN_GENOMES ss3798742690 Jul 12, 2019 (153)
16 KOGIC ss3943625266 Apr 25, 2020 (154)
17 TOMMO_GENOMICS ss5142040711 Apr 25, 2021 (155)
18 1000Genomes NC_000001.10 - 255924 Oct 11, 2018 (152)
19 The Danish reference pan genome NC_000001.10 - 255924 Apr 25, 2020 (154)
20 Korean Genome Project NC_000001.11 - 286173 Apr 25, 2020 (154)
21 Northern Sweden NC_000001.10 - 255924 Jul 12, 2019 (153)
22 8.3KJPN NC_000001.10 - 255924 Apr 25, 2021 (155)
23 ALFA NC_000001.11 - 286173 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
ss550903097 NC_000001.9:245786::TC NC_000001.11:286172:T:TCT (self)
ss287939226 NC_000001.9:245787::CT NC_000001.11:286172:T:TCT (self)
1203, 120176, 417, 10018, ss498763778, ss1367645251, ss1573867295, ss2030297686, ss2986144547, ss3726715552, ss5142040711 NC_000001.10:255923::TC NC_000001.11:286172:T:TCT (self)
3267, ss3063573450, ss3064385964, ss3065282439, ss3066352004, ss3646580825, ss3685991103, ss3798742690, ss3943625266 NC_000001.11:286172::TC NC_000001.11:286172:T:TCT (self)
9159696632 NC_000001.11:286172:T:TCT NC_000001.11:286172:T:TCT
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 rs199745078

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