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dbSNP Short Genetic Variations

Reference SNP (rs) Report

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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.

rs199474352

Current Build 151

Released July 17, 2018

Organism
Homo sapiens
Position
chr6:29942779 (GRCh38.p7) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
None
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HLA-A : Missense 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.p7 chr 6 NC_000006.12:g.29942779C>G
GRCh37.p13 chr 6 NC_000006.11:g.29910556C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1422201C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1422307C>G
HLA-A RefSeqGene NG_029217.2:g.5314C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1200526C>G
GRCh37.p13 chr 6 fix patch HG1322_PATCH NW_003871063.1:g.176703C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1197738C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1203334C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1198332C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1203917C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1240592C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1239890C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1197320C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1202940C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.1286859C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.1292444C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1150442C>G
Gene: HLA-A, major histocompatibility complex, class I, A (plus strand)
Molecule type Change Amino acid[Codon] SO Term
HLA-A transcript variant 1 (A*03:01:0:01) NM_002116.7:c.96C>G F [TTC] > L [TTG] Coding Sequence Variant
HLA class I histocompatibility antigen, A-1 alpha chain A*03:01:0:01 precursor NP_002107.3:p.Phe...

NP_002107.3:p.Phe32Leu

F (Phe) > L (Leu) Missense 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").

None
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 Note
GRCh38.p7 chr 6 NC_000006.12:g.29942779C= NC_000006.12:g.29942779C>G
GRCh37.p13 chr 6 NC_000006.11:g.29910556C= NC_000006.11:g.29910556C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1422201C= NT_113891.3:g.1422201C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1422307C= NT_113891.2:g.1422307C>G
HLA-A RefSeqGene NG_029217.2:g.5314C= NG_029217.2:g.5314C>G
HLA-A transcript variant 1 (A*03:01:0:01) NM_002116.7:c.96C= NM_002116.7:c.96C>G
HLA-A transcript variant 2 (A*01:01:01:01) NM_001242758.1:c.96C= NM_001242758.1:c.96C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.1200526C= NT_167244.2:g.1200526C>G
GRCh37.p13 chr 6 fix patch HG1322_PATCH NW_003871063.1:g.176703C= NW_003871063.1:g.176703C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.1197738C= NT_167248.2:g.1197738C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.1203334C= NT_167248.1:g.1203334C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.1198332C= NT_167245.2:g.1198332C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.1203917C= NT_167245.1:g.1203917C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.1240592C= NT_167249.2:g.1240592C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.1239890C= NT_167249.1:g.1239890C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.1197320C= NT_167246.2:g.1197320C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.1202940C= NT_167246.1:g.1202940C>G
GRCh38.p7 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.1286859C= NT_167247.2:g.1286859C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.1292444C= NT_167247.1:g.1292444C>G
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.1150442C= NT_167244.1:g.1150442C>G
HLA-A transcript variant X4 XM_005275331.2:c.87C= XM_005275331.2:c.87C>G
HLA-A transcript variant X3 XM_005275331.1:c.87C= XM_005275331.1:c.87C>G
HLA-A transcript variant X3 XR_430999.1:n.88C= XR_430999.1:n.88C>G
HLA-A transcript variant X2 XM_017030288.1:c.87C= XM_017030288.1:c.87C>G
HLA class I histocompatibility antigen, A-1 alpha chain A*03:01:0:01 precursor NP_002107.3:p.Phe32= NP_002107.3:p.Phe32Leu
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#.

1 SubSNP submissions
No Submitter Submission ID Date (Build)
1 DBMHC ss539214467 Oct 04, 2012 (137)
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
ss539214467 NC_000006.12:29942778:C= NC_000006.12:29942778:C= (self)
ss539214467 NC_000006.12:29942778:C>G NC_000006.12:29942778:C>G (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 rs199474352

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: 0.1.4.post833+d3ba21e