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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.

rs200227753

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:136922614 (GRCh38.p14) 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>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000019 (5/264690, TOPMED)
T=0.00006 (2/35368, ALFA)
T=0.0003 (2/6404, 1000G_30x) (+ 1 more)
T=0.0002 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SLC35D3 : Synonymous Variant
Publications
0 citations
Genomic View
See rs on genome

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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 35368 C=0.99994 T=0.00006
European Sub 26528 C=1.00000 T=0.00000
African Sub 2918 C=0.9993 T=0.0007
African Others Sub 114 C=1.000 T=0.000
African American Sub 2804 C=0.9993 T=0.0007
Asian Sub 112 C=1.000 T=0.000
East Asian Sub 86 C=1.00 T=0.00
Other Asian Sub 26 C=1.00 T=0.00
Latin American 1 Sub 500 C=1.000 T=0.000
Latin American 2 Sub 628 C=1.000 T=0.000
South Asian Sub 98 C=1.00 T=0.00
Other Sub 4584 C=1.0000 T=0.0000


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 264690 C=0.999981 T=0.000019
Allele Frequency Aggregator Total Global 35368 C=0.99994 T=0.00006
Allele Frequency Aggregator European Sub 26528 C=1.00000 T=0.00000
Allele Frequency Aggregator Other Sub 4584 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2918 C=0.9993 T=0.0007
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 C=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 C=0.9997 T=0.0003
1000Genomes_30x African Sub 1786 C=0.9989 T=0.0011
1000Genomes_30x Europe Sub 1266 C=1.0000 T=0.0000
1000Genomes_30x South Asian Sub 1202 C=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 C=1.0000 T=0.0000
1000Genomes_30x American Sub 980 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=0.9998 T=0.0002
1000Genomes African Sub 1322 C=0.9992 T=0.0008
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=1.0000 T=0.0000
1000Genomes South Asian Sub 978 C=1.000 T=0.000
1000Genomes American Sub 694 C=1.000 T=0.000
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.p14 chr 6 NC_000006.12:g.136922614C>G
GRCh38.p14 chr 6 NC_000006.12:g.136922614C>T
GRCh37.p13 chr 6 NC_000006.11:g.137243752C>G
GRCh37.p13 chr 6 NC_000006.11:g.137243752C>T
Gene: SLC35D3, solute carrier family 35 member D3 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SLC35D3 transcript NM_001008783.3:c.186C>G L [CTC] > L [CTG] Coding Sequence Variant
solute carrier family 35 member D3 NP_001008783.1:p.Leu62= L (Leu) > L (Leu) Synonymous Variant
SLC35D3 transcript NM_001008783.3:c.186C>T L [CTC] > L [CTT] Coding Sequence Variant
solute carrier family 35 member D3 NP_001008783.1:p.Leu62= L (Leu) > L (Leu) Synonymous 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

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= G T
GRCh38.p14 chr 6 NC_000006.12:g.136922614= NC_000006.12:g.136922614C>G NC_000006.12:g.136922614C>T
GRCh37.p13 chr 6 NC_000006.11:g.137243752= NC_000006.11:g.137243752C>G NC_000006.11:g.137243752C>T
SLC35D3 transcript NM_001008783.3:c.186= NM_001008783.3:c.186C>G NM_001008783.3:c.186C>T
SLC35D3 transcript NM_001008783.2:c.186= NM_001008783.2:c.186C>G NM_001008783.2:c.186C>T
SLC35D3 transcript NM_001008783.1:c.186= NM_001008783.1:c.186C>G NM_001008783.1:c.186C>T
solute carrier family 35 member D3 NP_001008783.1:p.Leu62= NP_001008783.1:p.Leu62= NP_001008783.1:p.Leu62=
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#.

12 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss488848645 May 04, 2012 (137)
2 1000GENOMES ss1322480507 Aug 21, 2014 (142)
3 EVA_EXAC ss1688513517 Apr 01, 2015 (144)
4 EVA_EXAC ss1688513518 Apr 01, 2015 (144)
5 GNOMAD ss2736089153 Nov 08, 2017 (151)
6 TOPMED ss4723675280 Apr 26, 2021 (155)
7 1000G_HIGH_COVERAGE ss5270532444 Oct 13, 2022 (156)
8 EVA ss5369344022 Oct 13, 2022 (156)
9 1000G_HIGH_COVERAGE ss5557569811 Oct 13, 2022 (156)
10 EVA ss5886165423 Oct 13, 2022 (156)
11 EVA ss5970360583 Oct 13, 2022 (156)
12 EVA ss5970360584 Oct 13, 2022 (156)
13 1000Genomes NC_000006.11 - 137243752 Oct 12, 2018 (152)
14 1000Genomes_30x NC_000006.12 - 136922614 Oct 13, 2022 (156)
15 ExAC

Submission ignored due to conflicting rows:
Row 8562063 (NC_000006.11:137243751:C:C 111641/111642, NC_000006.11:137243751:C:G 1/111642)
Row 8562064 (NC_000006.11:137243751:C:C 111639/111642, NC_000006.11:137243751:C:T 3/111642)

- Oct 12, 2018 (152)
16 ExAC

Submission ignored due to conflicting rows:
Row 8562063 (NC_000006.11:137243751:C:C 111641/111642, NC_000006.11:137243751:C:G 1/111642)
Row 8562064 (NC_000006.11:137243751:C:C 111639/111642, NC_000006.11:137243751:C:T 3/111642)

- Oct 12, 2018 (152)
17 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 5240558 (NC_000006.11:137243751:C:C 243557/243558, NC_000006.11:137243751:C:G 1/243558)
Row 5240559 (NC_000006.11:137243751:C:C 243551/243558, NC_000006.11:137243751:C:T 7/243558)

- Jul 13, 2019 (153)
18 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 5240558 (NC_000006.11:137243751:C:C 243557/243558, NC_000006.11:137243751:C:G 1/243558)
Row 5240559 (NC_000006.11:137243751:C:C 243551/243558, NC_000006.11:137243751:C:T 7/243558)

- Jul 13, 2019 (153)
19 TopMed NC_000006.12 - 136922614 Apr 26, 2021 (155)
20 ALFA NC_000006.12 - 136922614 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1688513518, ss2736089153 NC_000006.11:137243751:C:G NC_000006.12:136922613:C:G (self)
34357362, ss488848645, ss1322480507, ss1688513517, ss2736089153, ss5369344022, ss5970360583, ss5970360584 NC_000006.11:137243751:C:T NC_000006.12:136922613:C:T (self)
45095746, 561052838, 638501393, ss4723675280, ss5270532444, ss5557569811, ss5886165423 NC_000006.12:136922613:C:T NC_000006.12:136922613: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 rs200227753

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.post761+d5e8e07