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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.

rs10399749

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:55299 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.33404 (5515/16510, 8.3KJPN)
T=0.0492 (378/7688, ALFA)
T=0.3538 (1019/2880, KOREAN) (+ 8 more)
T=0.3624 (653/1802, Korea1K)
T=0.171 (171/998, GoNL)
T=0.310 (139/448, NorthernSweden)
T=0.000 (0/314, HapMap)
C=0.399 (95/238, SGDP_PRJ)
T=0.274 (46/168, Qatari)
T=0.30 (9/30, GENOME_DK)
C=0.33 (4/12, Siberian)
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.55299C>A
GRCh38.p13 chr 1 NC_000001.11:g.55299C>T
GRCh37.p13 chr 1 NC_000001.10:g.55299C>A
GRCh37.p13 chr 1 NC_000001.10:g.55299C>T
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 7688 C=0.9508 A=0.0000, T=0.0492
European Sub 5654 C=0.9759 A=0.0000, T=0.0241
African Sub 1218 C=0.8013 A=0.0000, T=0.1987
African Others Sub 46 C=0.78 A=0.00, T=0.22
African American Sub 1172 C=0.8020 A=0.0000, T=0.1980
Asian Sub 38 C=1.00 A=0.00, T=0.00
East Asian Sub 28 C=1.00 A=0.00, T=0.00
Other Asian Sub 10 C=1.0 A=0.0, T=0.0
Latin American 1 Sub 100 C=1.00 A=0.00, T=0.00
Latin American 2 Sub 346 C=1.000 A=0.000, T=0.000
South Asian Sub 66 C=1.00 A=0.00, T=0.00
Other Sub 266 C=1.000 A=0.000, T=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").

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Study Population Group Sample Size Ref Allele Alt Allele
8.3KJPN JAPANESE Study-wide 16510 C=0.66596 T=0.33404
KOREAN population from KRGDB KOREAN Study-wide 2880 C=0.6462 T=0.3538
Korean Genome Project KOREAN Study-wide 1802 C=0.6376 T=0.3624
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.829 T=0.171
Northern Sweden ACPOP Study-wide 448 C=0.690 T=0.310
HapMap Global Study-wide 314 C=1.000 T=0.000
HapMap American Sub 114 C=1.000 T=0.000
HapMap African Sub 112 C=1.000 T=0.000
HapMap Asian Sub 88 C=1.00 T=0.00
SGDP_PRJ Global Study-wide 238 C=0.399 T=0.601
Qatari Global Study-wide 168 C=0.726 T=0.274
The Danish reference pan genome Danish Study-wide 30 C=0.70 T=0.30
Siberian Global Study-wide 12 C=0.33 T=0.67
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 C= A T
GRCh38.p13 chr 1 NC_000001.11:g.55299= NC_000001.11:g.55299C>A NC_000001.11:g.55299C>T
GRCh37.p13 chr 1 NC_000001.10:g.55299= NC_000001.10:g.55299C>A NC_000001.10:g.55299C>T
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#.

28 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss14687333 Dec 05, 2003 (119)
2 CSHL-HAPMAP ss16401979 Feb 27, 2004 (120)
3 ILLUMINA-UK ss118438121 Feb 14, 2009 (130)
4 GMI ss154521915 Dec 01, 2009 (131)
5 1000GENOMES ss218190319 Jul 14, 2010 (132)
6 1000GENOMES ss230395378 Jul 14, 2010 (132)
7 1000GENOMES ss238114927 Jul 15, 2010 (132)
8 GMI ss275679902 May 04, 2012 (137)
9 SSMP ss647514821 Apr 25, 2013 (138)
10 EVA-GONL ss974768743 Aug 21, 2014 (142)
11 DDI ss1425684544 Apr 01, 2015 (144)
12 EVA_GENOME_DK ss1573850712 Apr 01, 2015 (144)
13 HAMMER_LAB ss1793705023 Sep 08, 2015 (146)
14 WEILL_CORNELL_DGM ss1917958223 Feb 12, 2016 (147)
15 GENOMED ss1966667266 Jul 19, 2016 (147)
16 USC_VALOUEV ss2147483701 Dec 20, 2016 (150)
17 GRF ss2697372977 Nov 08, 2017 (151)
18 GNOMAD ss2750603671 Nov 08, 2017 (151)
19 SWEGEN ss2986141909 Nov 08, 2017 (151)
20 TOPMED ss3066320698 Nov 08, 2017 (151)
21 EVA_DECODE ss3685990385 Jul 12, 2019 (153)
22 ACPOP ss3726715181 Jul 12, 2019 (153)
23 EVA ss3745720524 Jul 12, 2019 (153)
24 EVA ss3825981326 Apr 25, 2020 (154)
25 SGDP_PRJ ss3847983921 Apr 25, 2020 (154)
26 KRGDB ss3892823768 Apr 25, 2020 (154)
27 KOGIC ss3943622540 Apr 25, 2020 (154)
28 TOMMO_GENOMICS ss5142032637 Apr 25, 2021 (155)
29 The Danish reference pan genome NC_000001.10 - 55299 Apr 25, 2020 (154)
30 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 3944 (NC_000001.11:55298:C:A 1/101532)
Row 3945 (NC_000001.11:55298:C:T 32371/100838)

- Apr 25, 2021 (155)
31 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 3944 (NC_000001.11:55298:C:A 1/101532)
Row 3945 (NC_000001.11:55298:C:T 32371/100838)

- Apr 25, 2021 (155)
32 Genome of the Netherlands Release 5 NC_000001.10 - 55299 Apr 25, 2020 (154)
33 HapMap NC_000001.11 - 55299 Apr 25, 2020 (154)
34 KOREAN population from KRGDB NC_000001.10 - 55299 Apr 25, 2020 (154)
35 Korean Genome Project NC_000001.11 - 55299 Apr 25, 2020 (154)
36 Northern Sweden NC_000001.10 - 55299 Jul 12, 2019 (153)
37 Qatari NC_000001.10 - 55299 Apr 25, 2020 (154)
38 SGDP_PRJ NC_000001.10 - 55299 Apr 25, 2020 (154)
39 Siberian NC_000001.10 - 55299 Apr 25, 2020 (154)
40 8.3KJPN NC_000001.10 - 55299 Apr 25, 2021 (155)
41 ALFA NC_000001.11 - 55299 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
4928180230 NC_000001.11:55298:C:A NC_000001.11:55298:C:A
ss118438121, ss275679902 NC_000001.9:45161:C:T NC_000001.11:55298:C:T (self)
1357946, 9, 1162, 46, 153, 901, 55, 1944, ss218190319, ss230395378, ss238114927, ss647514821, ss974768743, ss1425684544, ss1573850712, ss1793705023, ss1917958223, ss1966667266, ss2147483701, ss2697372977, ss2750603671, ss2986141909, ss3726715181, ss3745720524, ss3825981326, ss3847983921, ss3892823768, ss5142032637 NC_000001.10:55298:C:T NC_000001.11:55298:C:T (self)
1, 541, 4928180230, ss3066320698, ss3685990385, ss3943622540 NC_000001.11:55298:C:T NC_000001.11:55298:C:T (self)
ss14687333, ss16401979 NT_077402.1:45161:C:T NC_000001.11:55298:C:T (self)
ss154521915 NT_077402.2:45298:C:T NC_000001.11:55298:C:T (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 rs10399749

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