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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.

rs1217691063

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:11796309 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000008 (2/264690, TOPMED)
G=0.000004 (1/251488, GnomAD_exome)
G=0.000007 (1/140270, GnomAD) (+ 1 more)
G=0.00006 (2/32062, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MTHFR : 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.p13 chr 1 NC_000001.11:g.11796309A>G
GRCh37.p13 chr 1 NC_000001.10:g.11856366A>G
MTHFR RefSeqGene (LRG_726) NG_013351.1:g.14795T>C
Gene: MTHFR, methylenetetrahydrofolate reductase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MTHFR transcript variant 2 NM_005957.5:c.677T>C I [ATC] > T [ACC] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform 2 NP_005948.3:p.Ile226Thr I (Ile) > T (Thr) Missense Variant
MTHFR transcript variant 1 NM_001330358.2:c.800T>C I [ATC] > T [ACC] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform 1 NP_001317287.1:p.Ile267Thr I (Ile) > T (Thr) Missense Variant
MTHFR transcript variant X4 XM_005263462.4:c.677T>C I [ATC] > T [ACC] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X3 XP_005263519.1:p.Ile226Thr I (Ile) > T (Thr) Missense Variant
MTHFR transcript variant X1 XM_011541495.3:c.797T>C I [ATC] > T [ACC] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X1 XP_011539797.1:p.Ile266Thr I (Ile) > T (Thr) Missense Variant
MTHFR transcript variant X2 XM_011541496.3:c.800T>C I [ATC] > T [ACC] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X2 XP_011539798.1:p.Ile267Thr I (Ile) > T (Thr) Missense Variant
MTHFR transcript variant X3 XM_005263460.5:c.677T>C I [ATC] > T [ACC] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X3 XP_005263517.1:p.Ile226Thr I (Ile) > T (Thr) Missense Variant
MTHFR transcript variant X5 XM_017001328.2:c.800T>C I [ATC] > T [ACC] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X4 XP_016856817.1:p.Ile267Thr I (Ile) > T (Thr) Missense Variant
MTHFR transcript variant X6 XM_005263463.4:c.431T>C I [ATC] > T [ACC] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X5 XP_005263520.1:p.Ile144Thr I (Ile) > T (Thr) Missense Variant
MTHFR transcript variant X7 XM_024447198.1:c.431T>C I [ATC] > T [ACC] Coding Sequence Variant
methylenetetrahydrofolate reductase isoform X5 XP_024302966.1:p.Ile144Thr I (Ile) > T (Thr) Missense Variant
MTHFR transcript variant X8 XR_002956640.1:n.1544T>C N/A Non Coding Transcript 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 (New)
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 32062 A=0.99994 G=0.00006
European Sub 23860 A=0.99992 G=0.00008
African Sub 2314 A=1.0000 G=0.0000
African Others Sub 84 A=1.00 G=0.00
African American Sub 2230 A=1.0000 G=0.0000
Asian Sub 108 A=1.000 G=0.000
East Asian Sub 84 A=1.00 G=0.00
Other Asian Sub 24 A=1.00 G=0.00
Latin American 1 Sub 500 A=1.000 G=0.000
Latin American 2 Sub 628 A=1.000 G=0.000
South Asian Sub 94 A=1.00 G=0.00
Other Sub 4558 A=1.0000 G=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 A=0.999992 G=0.000008
gnomAD - Exomes Global Study-wide 251488 A=0.999996 G=0.000004
gnomAD - Exomes European Sub 135414 A=1.000000 G=0.000000
gnomAD - Exomes Asian Sub 49008 A=1.00000 G=0.00000
gnomAD - Exomes American Sub 34592 A=0.99997 G=0.00003
gnomAD - Exomes African Sub 16256 A=1.00000 G=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6138 A=1.0000 G=0.0000
gnomAD - Genomes Global Study-wide 140270 A=0.999993 G=0.000007
gnomAD - Genomes European Sub 75954 A=0.99999 G=0.00001
gnomAD - Genomes African Sub 42066 A=1.00000 G=0.00000
gnomAD - Genomes American Sub 13652 A=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3130 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2144 A=1.0000 G=0.0000
Allele Frequency Aggregator Total Global 32062 A=0.99994 G=0.00006
Allele Frequency Aggregator European Sub 23860 A=0.99992 G=0.00008
Allele Frequency Aggregator Other Sub 4558 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2314 A=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 A=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 108 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 94 A=1.00 G=0.00
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 A= G
GRCh38.p13 chr 1 NC_000001.11:g.11796309= NC_000001.11:g.11796309A>G
GRCh37.p13 chr 1 NC_000001.10:g.11856366= NC_000001.10:g.11856366A>G
MTHFR RefSeqGene (LRG_726) NG_013351.1:g.14795= NG_013351.1:g.14795T>C
MTHFR transcript variant 2 NM_005957.5:c.677= NM_005957.5:c.677T>C
MTHFR transcript variant 2 NM_005957.4:c.677= NM_005957.4:c.677T>C
MTHFR transcript variant 1 NM_001330358.2:c.800= NM_001330358.2:c.800T>C
MTHFR transcript variant 1 NM_001330358.1:c.800= NM_001330358.1:c.800T>C
MTHFR transcript variant X3 XM_005263460.5:c.677= XM_005263460.5:c.677T>C
MTHFR transcript variant X3 XM_005263460.1:c.677= XM_005263460.1:c.677T>C
MTHFR transcript variant X6 XM_005263463.4:c.431= XM_005263463.4:c.431T>C
MTHFR transcript variant X6 XM_005263463.1:c.431= XM_005263463.1:c.431T>C
MTHFR transcript variant X4 XM_005263462.4:c.677= XM_005263462.4:c.677T>C
MTHFR transcript variant X5 XM_005263462.1:c.677= XM_005263462.1:c.677T>C
MTHFR transcript variant X1 XM_011541495.3:c.797= XM_011541495.3:c.797T>C
MTHFR transcript variant X2 XM_011541496.3:c.800= XM_011541496.3:c.800T>C
MTHFR transcript variant X5 XM_017001328.2:c.800= XM_017001328.2:c.800T>C
MTHFR transcript variant X8 XR_002956640.1:n.1544= XR_002956640.1:n.1544T>C
MTHFR transcript variant X7 XM_024447198.1:c.431= XM_024447198.1:c.431T>C
methylenetetrahydrofolate reductase isoform 2 NP_005948.3:p.Ile226= NP_005948.3:p.Ile226Thr
methylenetetrahydrofolate reductase isoform 1 NP_001317287.1:p.Ile267= NP_001317287.1:p.Ile267Thr
methylenetetrahydrofolate reductase isoform X3 XP_005263517.1:p.Ile226= XP_005263517.1:p.Ile226Thr
methylenetetrahydrofolate reductase isoform X5 XP_005263520.1:p.Ile144= XP_005263520.1:p.Ile144Thr
methylenetetrahydrofolate reductase isoform X3 XP_005263519.1:p.Ile226= XP_005263519.1:p.Ile226Thr
methylenetetrahydrofolate reductase isoform X1 XP_011539797.1:p.Ile266= XP_011539797.1:p.Ile266Thr
methylenetetrahydrofolate reductase isoform X2 XP_011539798.1:p.Ile267= XP_011539798.1:p.Ile267Thr
methylenetetrahydrofolate reductase isoform X4 XP_016856817.1:p.Ile267= XP_016856817.1:p.Ile267Thr
methylenetetrahydrofolate reductase isoform X5 XP_024302966.1:p.Ile144= XP_024302966.1:p.Ile144Thr
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#.

3 SubSNP, 4 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2731121851 Nov 08, 2017 (151)
2 GNOMAD ss3988405118 Apr 25, 2021 (155)
3 TOPMED ss4439376293 Apr 25, 2021 (155)
4 gnomAD - Genomes NC_000001.11 - 11796309 Apr 25, 2021 (155)
5 gnomAD - Exomes NC_000001.10 - 11856366 Jul 12, 2019 (153)
6 TopMed NC_000001.11 - 11796309 Apr 25, 2021 (155)
7 ALFA NC_000001.11 - 11796309 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
138119, ss2731121851 NC_000001.10:11856365:A:G NC_000001.11:11796308:A:G (self)
2629211, 2982628, 608376975, ss3988405118, ss4439376293 NC_000001.11:11796308:A:G NC_000001.11:11796308:A:G
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 rs1217691063

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