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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.

rs9550376

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr13:28473733 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.14222 (5925/41662, GnomAD)
A=0.09459 (1511/15974, 8.3KJPN)
A=0.0782 (368/4706, ALFA) (+ 8 more)
A=0.2863 (839/2930, KOREAN)
A=0.0635 (111/1748, Korea1K)
A=0.349 (348/998, GoNL)
A=0.171 (102/596, NorthernSweden)
G=0.478 (175/366, SGDP_PRJ)
A=0.394 (85/216, Qatari)
A=0.37 (14/38, GENOME_DK)
G=0.45 (10/22, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
FLT1 : 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 13 NC_000013.11:g.28473733G>A
GRCh38.p13 chr 13 NC_000013.11:g.28473733G>C
GRCh37.p13 chr 13 NC_000013.10:g.29047870G>A
GRCh37.p13 chr 13 NC_000013.10:g.29047870G>C
FLT1 RefSeqGene (LRG_425) NG_012003.1:g.26396C>T
FLT1 RefSeqGene (LRG_425) NG_012003.1:g.26396C>G
Gene: FLT1, fms related receptor tyrosine kinase 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
FLT1 transcript variant 2 NM_001159920.2:c.65-6116C…

NM_001159920.2:c.65-6116C>T

N/A Intron Variant
FLT1 transcript variant 3 NM_001160030.2:c.65-6116C…

NM_001160030.2:c.65-6116C>T

N/A Intron Variant
FLT1 transcript variant 4 NM_001160031.1:c.65-6116C…

NM_001160031.1:c.65-6116C>T

N/A Intron Variant
FLT1 transcript variant 1 NM_002019.4:c.65-6116C>T N/A Intron Variant
FLT1 transcript variant X2 XM_011535014.1:c.65-6116C…

XM_011535014.1:c.65-6116C>T

N/A Intron Variant
FLT1 transcript variant X1 XM_017020485.1:c.65-6116C…

XM_017020485.1:c.65-6116C>T

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 4706 G=0.9218 A=0.0782, C=0.0000
European Sub 2762 G=0.9196 A=0.0804, C=0.0000
African Sub 1384 G=0.8952 A=0.1048, C=0.0000
African Others Sub 48 G=0.90 A=0.10, C=0.00
African American Sub 1336 G=0.8952 A=0.1048, C=0.0000
Asian Sub 60 G=1.00 A=0.00, C=0.00
East Asian Sub 42 G=1.00 A=0.00, C=0.00
Other Asian Sub 18 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 52 G=1.00 A=0.00, C=0.00
Latin American 2 Sub 260 G=1.000 A=0.000, C=0.000
South Asian Sub 28 G=1.00 A=0.00, C=0.00
Other Sub 160 G=0.994 A=0.006, C=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 41662 G=0.85778 A=0.14222
gnomAD - Genomes European Sub 26844 G=0.86649 A=0.13351
gnomAD - Genomes African Sub 8702 G=0.8210 A=0.1790
gnomAD - Genomes American Sub 3224 G=0.8824 A=0.1176
gnomAD - Genomes Ashkenazi Jewish Sub 1300 G=0.8092 A=0.1908
gnomAD - Genomes East Asian Sub 968 G=0.931 A=0.069
gnomAD - Genomes Other Sub 624 G=0.857 A=0.143
8.3KJPN JAPANESE Study-wide 15974 G=0.90541 A=0.09459
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.7137 A=0.2863
Korean Genome Project KOREAN Study-wide 1748 G=0.9365 A=0.0635
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.651 A=0.349
Northern Sweden ACPOP Study-wide 596 G=0.829 A=0.171
SGDP_PRJ Global Study-wide 366 G=0.478 A=0.522
Qatari Global Study-wide 216 G=0.606 A=0.394
The Danish reference pan genome Danish Study-wide 38 G=0.63 A=0.37
Siberian Global Study-wide 22 G=0.45 A=0.55
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 G= A C
GRCh38.p13 chr 13 NC_000013.11:g.28473733= NC_000013.11:g.28473733G>A NC_000013.11:g.28473733G>C
GRCh37.p13 chr 13 NC_000013.10:g.29047870= NC_000013.10:g.29047870G>A NC_000013.10:g.29047870G>C
FLT1 RefSeqGene (LRG_425) NG_012003.1:g.26396= NG_012003.1:g.26396C>T NG_012003.1:g.26396C>G
FLT1 transcript variant 2 NM_001159920.1:c.65-6116= NM_001159920.1:c.65-6116C>T NM_001159920.1:c.65-6116C>G
FLT1 transcript variant 2 NM_001159920.2:c.65-6116= NM_001159920.2:c.65-6116C>T NM_001159920.2:c.65-6116C>G
FLT1 transcript variant 3 NM_001160030.1:c.65-6116= NM_001160030.1:c.65-6116C>T NM_001160030.1:c.65-6116C>G
FLT1 transcript variant 3 NM_001160030.2:c.65-6116= NM_001160030.2:c.65-6116C>T NM_001160030.2:c.65-6116C>G
FLT1 transcript variant 4 NM_001160031.1:c.65-6116= NM_001160031.1:c.65-6116C>T NM_001160031.1:c.65-6116C>G
FLT1 transcript variant 1 NM_002019.4:c.65-6116= NM_002019.4:c.65-6116C>T NM_002019.4:c.65-6116C>G
FLT1 transcript variant X2 XM_011535014.1:c.65-6116= XM_011535014.1:c.65-6116C>T XM_011535014.1:c.65-6116C>G
FLT1 transcript variant X1 XM_017020485.1:c.65-6116= XM_017020485.1:c.65-6116C>T XM_017020485.1:c.65-6116C>G
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#.

22 SubSNP, 11 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss13254262 Dec 05, 2003 (119)
2 HGSV ss82459314 Dec 14, 2007 (130)
3 HUMANGENOME_JCVI ss97145361 Feb 04, 2009 (130)
4 1000GENOMES ss337782485 May 09, 2011 (134)
5 GMI ss475790955 May 04, 2012 (137)
6 SSMP ss659166631 Apr 25, 2013 (138)
7 EVA-GONL ss990227179 Aug 21, 2014 (142)
8 EVA_GENOME_DK ss1576694136 Apr 01, 2015 (144)
9 WEILL_CORNELL_DGM ss1933596084 Feb 12, 2016 (147)
10 USC_VALOUEV ss2155918338 Dec 20, 2016 (150)
11 GRF ss2700290528 Nov 08, 2017 (151)
12 TOPMED ss3188754594 Nov 08, 2017 (151)
13 CSHL ss3350381357 Nov 08, 2017 (151)
14 URBANLAB ss3649996179 Oct 12, 2018 (152)
15 EVA_DECODE ss3694989475 Jul 13, 2019 (153)
16 ACPOP ss3739611366 Jul 13, 2019 (153)
17 EVA ss3751274422 Jul 13, 2019 (153)
18 SGDP_PRJ ss3879658436 Apr 27, 2020 (154)
19 KRGDB ss3928479829 Apr 27, 2020 (154)
20 KOGIC ss3973266023 Apr 27, 2020 (154)
21 GNOMAD ss4263235175 Apr 26, 2021 (155)
22 TOMMO_GENOMICS ss5209311780 Apr 26, 2021 (155)
23 The Danish reference pan genome NC_000013.10 - 29047870 Apr 27, 2020 (154)
24 gnomAD - Genomes NC_000013.11 - 28473733 Apr 26, 2021 (155)
25 Genome of the Netherlands Release 5 NC_000013.10 - 29047870 Apr 27, 2020 (154)
26 KOREAN population from KRGDB NC_000013.10 - 29047870 Apr 27, 2020 (154)
27 Korean Genome Project NC_000013.11 - 28473733 Apr 27, 2020 (154)
28 Northern Sweden NC_000013.10 - 29047870 Jul 13, 2019 (153)
29 Qatari NC_000013.10 - 29047870 Apr 27, 2020 (154)
30 SGDP_PRJ NC_000013.10 - 29047870 Apr 27, 2020 (154)
31 Siberian NC_000013.10 - 29047870 Apr 27, 2020 (154)
32 8.3KJPN NC_000013.10 - 29047870 Apr 26, 2021 (155)
33 ALFA NC_000013.11 - 28473733 Apr 26, 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)
rs57049657 May 23, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82459314, ss475790955 NC_000013.9:27945869:G:A NC_000013.11:28473732:G:A (self)
3233890, 14983691, 35657223, 12896231, 15638014, 31675416, 8434692, 67281087, ss337782485, ss659166631, ss990227179, ss1576694136, ss1933596084, ss2155918338, ss2700290528, ss3350381357, ss3739611366, ss3751274422, ss3879658436, ss3928479829, ss5209311780 NC_000013.10:29047869:G:A NC_000013.11:28473732:G:A (self)
426353489, 29644024, 10107924864, ss3188754594, ss3649996179, ss3694989475, ss3973266023, ss4263235175 NC_000013.11:28473732:G:A NC_000013.11:28473732:G:A (self)
ss13254262 NT_009799.12:10027869:G:A NC_000013.11:28473732:G:A (self)
ss97145361 NT_024524.14:10027869:G:A NC_000013.11:28473732:G:A (self)
10107924864 NC_000013.11:28473732:G:C NC_000013.11:28473732:G:C
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 rs9550376

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