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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.

rs121913223

Current Build 154

Released April 21, 2020

Organism
Homo sapiens
Position
chr5:80633904 (GRCh38.p12) 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
T>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000004 (1/249832, GnomAD_exome)
A=0.00000 (0/78698, PAGE_STUDY)
Clinical Significance
Reported in ClinVar
Gene : Consequence
DHFR : Missense Variant
Publications
4 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.p12 chr 5 NC_000005.10:g.80633904T>A
GRCh37.p13 chr 5 NC_000005.9:g.79929723T>A
DHFR RefSeqGene NG_023304.1:g.26078A>T
Gene: DHFR, dihydrofolate reductase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
DHFR transcript variant 3 NM_001290357.2:c.369+3979…

NM_001290357.2:c.369+3979A>T

N/A Intron Variant
DHFR transcript variant 1 NM_000791.4:c.458A>T D [GAT] > V [GTT] Coding Sequence Variant
dihydrofolate reductase isoform 1 NP_000782.1:p.Asp153Val D (Asp) > V (Val) Missense Variant
DHFR transcript variant 2 NM_001290354.2:c.302A>T D [GAT] > V [GTT] Coding Sequence Variant
dihydrofolate reductase isoform 2 NP_001277283.1:p.Asp101Val D (Asp) > V (Val) Missense Variant
DHFR transcript variant 4 NR_110936.2:n.775A>T 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.

Allele: A (allele ID: 38629 )
ClinVar Accession Disease Names Clinical Significance
RCV000022525.25 Megaloblastic anemia due to dihydrofolate reductase deficiency Pathogenic
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
gnomAD - Exomes Global Study-wide 249832 T=0.999996 A=0.000004
gnomAD - Exomes European Sub 134854 T=0.999993 A=0.000007
gnomAD - Exomes Asian Sub 48856 T=1.00000 A=0.00000
gnomAD - Exomes American Sub 34490 T=1.00000 A=0.00000
gnomAD - Exomes African Sub 15510 T=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10064 T=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6058 T=1.0000 A=0.0000
The PAGE Study Global Study-wide 78698 T=1.00000 A=0.00000
The PAGE Study AfricanAmerican Sub 32516 T=1.00000 A=0.00000
The PAGE Study Mexican Sub 10810 T=1.00000 A=0.00000
The PAGE Study Asian Sub 8316 T=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 T=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4534 T=1.0000 A=0.0000
The PAGE Study Cuban Sub 4228 T=1.0000 A=0.0000
The PAGE Study Dominican Sub 3828 T=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 T=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 T=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 T=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 T=1.000 A=0.000
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 T= A
GRCh38.p12 chr 5 NC_000005.10:g.80633904= NC_000005.10:g.80633904T>A
GRCh37.p13 chr 5 NC_000005.9:g.79929723= NC_000005.9:g.79929723T>A
DHFR RefSeqGene NG_023304.1:g.26078= NG_023304.1:g.26078A>T
DHFR transcript variant 1 NM_000791.4:c.458= NM_000791.4:c.458A>T
DHFR transcript variant 1 NM_000791.3:c.458= NM_000791.3:c.458A>T
DHFR transcript variant 2 NM_001290354.2:c.302= NM_001290354.2:c.302A>T
DHFR transcript variant 2 NM_001290354.1:c.302= NM_001290354.1:c.302A>T
DHFR transcript variant 4 NR_110936.2:n.775= NR_110936.2:n.775A>T
DHFR transcript variant 4 NR_110936.1:n.773= NR_110936.1:n.773A>T
dihydrofolate reductase isoform 1 NP_000782.1:p.Asp153= NP_000782.1:p.Asp153Val
dihydrofolate reductase isoform 2 NP_001277283.1:p.Asp101= NP_001277283.1:p.Asp101Val
DHFR transcript variant 3 NM_001290357.2:c.369+3979= NM_001290357.2:c.369+3979A>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#.

7 SubSNP, 2 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 HCULM ss275515041 Nov 22, 2010 (133)
2 ILLUMINA ss1958799154 Feb 12, 2016 (147)
3 GNOMAD ss2735094356 Nov 08, 2017 (151)
4 ILLUMINA ss3022502121 Nov 08, 2017 (151)
5 ILLUMINA ss3652999014 Oct 12, 2018 (152)
6 ILLUMINA ss3726245139 Jul 13, 2019 (153)
7 PAGE_CC ss3771212041 Jul 13, 2019 (153)
8 gnomAD - Exomes NC_000005.9 - 79929723 Jul 13, 2019 (153)
9 The PAGE Study NC_000005.10 - 80633904 Jul 13, 2019 (153)
10 ClinVar RCV000022525.25 Oct 12, 2018 (152)
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
4213629, ss1958799154, ss2735094356, ss3022502121, ss3652999014 NC_000005.9:79929722:T:A NC_000005.10:80633903:T:A (self)
RCV000022525.25, 433510, ss275515041, ss3726245139, ss3771212041 NC_000005.10:80633903:T:A NC_000005.10:80633903:T:A (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

4 citations for rs121913223
PMID Title Author Year Journal
1060915 Dihydrofolate reductase deficiency causing megaloblastic anemia in two families. Tauro GP et al. 1976 The New England journal of medicine
1099447 Inborn errors of folate metabolism (first of two parts). Erbe RE et al. 1975 The New England journal of medicine
6700662 Hereditary abnormal transcobalamin II previously diagnosed as congenital dihydrofolate reductase deficiency. Hoffbrand AV et al. 1984 The New England journal of medicine
21310277 Dihydrofolate reductase deficiency due to a homozygous DHFR mutation causes megaloblastic anemia and cerebral folate deficiency leading to severe neurologic disease. Cario H et al. 2011 American journal of human genetics
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.post536+f5d31d6