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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1479416589

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr6:29659442 (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>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000008 (2/264690, TOPMED)
T=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MOG : Missense 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 14050 C=1.00000 T=0.00000 1.0 0.0 0.0 N/A
European Sub 9690 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Sub 2898 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 C=1.000 T=0.000 1.0 0.0 0.0 N/A
African American Sub 2784 C=1.0000 T=0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 C=1.000 T=0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=1.000 T=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=1.000 T=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 C=1.00 T=0.00 1.0 0.0 0.0 N/A
Other Sub 496 C=1.000 T=0.000 1.0 0.0 0.0 N/A


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=0.999992 T=0.000008
Allele Frequency Aggregator Total Global 14050 C=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 9690 C=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2898 C=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=1.000 T=0.000
Allele Frequency Aggregator Other Sub 496 C=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 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
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.29659442C>T
GRCh37.p13 chr 6 NC_000006.11:g.29627219C>T
MOG RefSeqGene NG_031873.1:g.7462C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1145912C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1146018C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.924941C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.930537C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.924986C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.930571C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.924558C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.930178C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.968472C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.967770C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.924822C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.930407C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.925149C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.930743C>T
Gene: MOG, myelin oligodendrocyte glycoprotein (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MOG transcript variant alpha6 NM_001170418.2:c.88+2145C…

NM_001170418.2:c.88+2145C>T

 		N/A Intron Variant
MOG transcript variant alpha5 NM_206814.6:c.88+2145C>T N/A Intron Variant
MOG transcript variant alpha1 NM_206809.4:c.212C>T P [CCC] > L [CTC] Coding Sequence Variant
myelin-oligodendrocyte glycoprotein isoform alpha1 precursor NP_996532.2:p.Pro71Leu P (Pro) > L (Leu) Missense Variant
MOG transcript variant alpha2 NM_206812.4:c.212C>T P [CCC] > L [CTC] Coding Sequence Variant
myelin-oligodendrocyte glycoprotein isoform alpha2 precursor NP_996535.2:p.Pro71Leu P (Pro) > L (Leu) Missense Variant
MOG transcript variant beta3 NM_206811.4:c.212C>T P [CCC] > L [CTC] Coding Sequence Variant
myelin-oligodendrocyte glycoprotein isoform beta3 precursor NP_996534.2:p.Pro71Leu P (Pro) > L (Leu) Missense Variant
MOG transcript variant alpha3 NM_001008228.3:c.212C>T P [CCC] > L [CTC] Coding Sequence Variant
myelin-oligodendrocyte glycoprotein isoform alpha3 precursor NP_001008229.1:p.Pro71Leu P (Pro) > L (Leu) Missense Variant
MOG transcript variant beta2 NM_001008229.3:c.212C>T P [CCC] > L [CTC] Coding Sequence Variant
myelin-oligodendrocyte glycoprotein isoform beta2 precursor NP_001008230.1:p.Pro71Leu P (Pro) > L (Leu) Missense Variant
MOG transcript variant 10 NM_001363610.2:c.212C>T P [CCC] > L [CTC] Coding Sequence Variant
myelin-oligodendrocyte glycoprotein isoform 10 precursor NP_001350539.1:p.Pro71Leu P (Pro) > L (Leu) Missense Variant
MOG transcript variant beta1 NM_002433.5:c.212C>T P [CCC] > L [CTC] Coding Sequence Variant
myelin-oligodendrocyte glycoprotein isoform beta1 precursor NP_002424.3:p.Pro71Leu P (Pro) > L (Leu) Missense Variant
MOG transcript variant beta5 NM_206810.4:c.212C>T P [CCC] > L [CTC] Coding Sequence Variant
myelin-oligodendrocyte glycoprotein isoform beta5 precursor NP_996533.2:p.Pro71Leu P (Pro) > 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

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= T
GRCh38.p14 chr 6 NC_000006.12:g.29659442= NC_000006.12:g.29659442C>T
GRCh37.p13 chr 6 NC_000006.11:g.29627219= NC_000006.11:g.29627219C>T
MOG RefSeqGene NG_031873.1:g.7462= NG_031873.1:g.7462C>T
MOG transcript variant beta1 NM_002433.5:c.212= NM_002433.5:c.212C>T
MOG transcript variant beta1 NM_002433.4:c.212= NM_002433.4:c.212C>T
MOG transcript variant alpha1 NM_206809.4:c.212= NM_206809.4:c.212C>T
MOG transcript variant alpha1 NM_206809.3:c.212= NM_206809.3:c.212C>T
MOG transcript variant alpha2 NM_206812.4:c.212= NM_206812.4:c.212C>T
MOG transcript variant alpha2 NM_206812.3:c.212= NM_206812.3:c.212C>T
MOG transcript variant beta3 NM_206811.4:c.212= NM_206811.4:c.212C>T
MOG transcript variant beta3 NM_206811.3:c.212= NM_206811.3:c.212C>T
MOG transcript variant beta5 NM_206810.4:c.212= NM_206810.4:c.212C>T
MOG transcript variant beta5 NM_206810.3:c.212= NM_206810.3:c.212C>T
MOG transcript variant alpha3 NM_001008228.3:c.212= NM_001008228.3:c.212C>T
MOG transcript variant alpha3 NM_001008228.2:c.212= NM_001008228.2:c.212C>T
MOG transcript variant beta2 NM_001008229.3:c.212= NM_001008229.3:c.212C>T
MOG transcript variant beta2 NM_001008229.2:c.212= NM_001008229.2:c.212C>T
MOG transcript variant 10 NM_001363610.2:c.212= NM_001363610.2:c.212C>T
MOG transcript variant 10 NM_001363610.1:c.212= NM_001363610.1:c.212C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.3:g.1145912= NT_113891.3:g.1145912C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_COX_CTG1 NT_113891.2:g.1146018= NT_113891.2:g.1146018C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.2:g.924941= NT_167248.2:g.924941C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_QBL_CTG1 NT_167248.1:g.930537= NT_167248.1:g.930537C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.2:g.924986= NT_167245.2:g.924986C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_DBB_CTG1 NT_167245.1:g.930571= NT_167245.1:g.930571C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.2:g.924558= NT_167246.2:g.924558C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MANN_CTG1 NT_167246.1:g.930178= NT_167246.1:g.930178C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.2:g.968472= NT_167249.2:g.968472C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_SSTO_CTG1 NT_167249.1:g.967770= NT_167249.1:g.967770C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.2:g.924822= NT_167247.2:g.924822C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_MCF_CTG1 NT_167247.1:g.930407= NT_167247.1:g.930407C>T
GRCh38.p14 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.2:g.925149= NT_167244.2:g.925149C>T
GRCh37.p13 chr 6 alt locus HSCHR6_MHC_APD_CTG1 NT_167244.1:g.930743= NT_167244.1:g.930743C>T
MOG transcript variant beta4 NM_206813.3:c.212= NM_206813.3:c.212C>T
MOG transcript variant beta4 NM_206813.4:c.212= NM_206813.4:c.212C>T
MOG transcript variant beta4 NM_206813.2:c.212= NM_206813.2:c.212C>T
MOG transcript variant 6 NM_206813.1:c.131= NM_206813.1:c.131C>T
myelin-oligodendrocyte glycoprotein isoform beta1 precursor NP_002424.3:p.Pro71= NP_002424.3:p.Pro71Leu
myelin-oligodendrocyte glycoprotein isoform alpha1 precursor NP_996532.2:p.Pro71= NP_996532.2:p.Pro71Leu
myelin-oligodendrocyte glycoprotein isoform alpha2 precursor NP_996535.2:p.Pro71= NP_996535.2:p.Pro71Leu
myelin-oligodendrocyte glycoprotein isoform beta3 precursor NP_996534.2:p.Pro71= NP_996534.2:p.Pro71Leu
myelin-oligodendrocyte glycoprotein isoform beta5 precursor NP_996533.2:p.Pro71= NP_996533.2:p.Pro71Leu
myelin-oligodendrocyte glycoprotein isoform alpha3 precursor NP_001008229.1:p.Pro71= NP_001008229.1:p.Pro71Leu
myelin-oligodendrocyte glycoprotein isoform beta2 precursor NP_001008230.1:p.Pro71= NP_001008230.1:p.Pro71Leu
myelin-oligodendrocyte glycoprotein isoform 10 precursor NP_001350539.1:p.Pro71= NP_001350539.1:p.Pro71Leu
MOG transcript variant alpha6 NM_001170418.1:c.88+2145= NM_001170418.1:c.88+2145C>T
MOG transcript variant alpha6 NM_001170418.2:c.88+2145= NM_001170418.2:c.88+2145C>T
MOG transcript variant alpha5 NM_206814.5:c.88+2145= NM_206814.5:c.88+2145C>T
MOG transcript variant alpha5 NM_206814.6:c.88+2145= NM_206814.6:c.88+2145C>T
MOG transcript variant X4 XM_005249134.1:c.88+2145= XM_005249134.1:c.88+2145C>T
MOG transcript variant X5 XM_005249135.1:c.32+25= XM_005249135.1:c.32+25C>T
MOG transcript variant X7 XM_005249137.1:c.88+2145= XM_005249137.1:c.88+2145C>T
MOG transcript variant X4 XM_005272823.1:c.88+2143= XM_005272823.1:c.88+2143C>T
MOG transcript variant X5 XM_005272824.1:c.32+25= XM_005272824.1:c.32+25C>T
MOG transcript variant X8 XM_005272827.1:c.88+2143= XM_005272827.1:c.88+2143C>T
MOG transcript variant X4 XM_005274868.1:c.88+2143= XM_005274868.1:c.88+2143C>T
MOG transcript variant X5 XM_005274869.1:c.32+25= XM_005274869.1:c.32+25C>T
MOG transcript variant X8 XM_005274872.1:c.88+2143= XM_005274872.1:c.88+2143C>T
MOG transcript variant X4 XM_005274980.1:c.88+2144= XM_005274980.1:c.88+2144C>T
MOG transcript variant X5 XM_005274981.1:c.32+25= XM_005274981.1:c.32+25C>T
MOG transcript variant X8 XM_005274984.1:c.88+2144= XM_005274984.1:c.88+2144C>T
MOG transcript variant X4 XM_005275128.1:c.88+2144= XM_005275128.1:c.88+2144C>T
MOG transcript variant X5 XM_005275129.1:c.32+25= XM_005275129.1:c.32+25C>T
MOG transcript variant X8 XM_005275132.1:c.88+2144= XM_005275132.1:c.88+2144C>T
MOG transcript variant X4 XM_005275255.1:c.88+2144= XM_005275255.1:c.88+2144C>T
MOG transcript variant X5 XM_005275256.1:c.32+25= XM_005275256.1:c.32+25C>T
MOG transcript variant X8 XM_005275259.1:c.88+2144= XM_005275259.1:c.88+2144C>T
MOG transcript variant X4 XM_005275413.1:c.88+2144= XM_005275413.1:c.88+2144C>T
MOG transcript variant X5 XM_005275414.1:c.32+25= XM_005275414.1:c.32+25C>T
MOG transcript variant X8 XM_005275417.1:c.88+2144= XM_005275417.1:c.88+2144C>T
MOG transcript variant X4 XM_005275561.1:c.88+2140= XM_005275561.1:c.88+2140C>T
MOG transcript variant X5 XM_005275562.1:c.32+25= XM_005275562.1:c.32+25C>T
MOG transcript variant X8 XM_005275565.1:c.88+2140= XM_005275565.1:c.88+2140C>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#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 TOPMED ss4698008126 Apr 26, 2021 (155)
2 TopMed NC_000006.12 - 29659442 Apr 26, 2021 (155)
3 ALFA NC_000006.12 - 29659442 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
535385684, 9377935655, ss4698008126 NC_000006.12:29659441:C:T NC_000006.12:29659441: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 rs1479416589

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.post820+afb47a3d