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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.

rs1971280

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr12:56450132 (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
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000021 (3/140118, GnomAD)
A=0.00004 (1/28258, 14KJPN)
A=0.00000 (0/14050, ALFA) (+ 2 more)
T=0.00000 (0/14050, ALFA)
T=0.000 (0/328, HapMap)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MIP : 3 Prime UTR Variant
TIMELESS : 2KB Upstream 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 14050 G=1.00000 A=0.00000, T=0.00000
European Sub 9690 G=1.0000 A=0.0000, T=0.0000
African Sub 2898 G=1.0000 A=0.0000, T=0.0000
African Others Sub 114 G=1.000 A=0.000, T=0.000
African American Sub 2784 G=1.0000 A=0.0000, T=0.0000
Asian Sub 112 G=1.000 A=0.000, T=0.000
East Asian Sub 86 G=1.00 A=0.00, T=0.00
Other Asian Sub 26 G=1.00 A=0.00, T=0.00
Latin American 1 Sub 146 G=1.000 A=0.000, T=0.000
Latin American 2 Sub 610 G=1.000 A=0.000, T=0.000
South Asian Sub 98 G=1.00 A=0.00, T=0.00
Other Sub 496 G=1.000 A=0.000, T=0.000


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 - Genomes Global Study-wide 140118 G=0.999979 T=0.000021
gnomAD - Genomes European Sub 75900 G=1.00000 T=0.00000
gnomAD - Genomes African Sub 41984 G=1.00000 T=0.00000
gnomAD - Genomes American Sub 13622 G=0.99978 T=0.00022
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 T=0.0000
14KJPN JAPANESE Study-wide 28258 G=0.99996 A=0.00004
Allele Frequency Aggregator Total Global 14050 G=1.00000 A=0.00000, T=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 A=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00, T=0.00
HapMap Global Study-wide 328 G=1.000 T=0.000
HapMap African Sub 120 G=1.000 T=0.000
HapMap American Sub 118 G=1.000 T=0.000
HapMap Asian Sub 90 G=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 12 NC_000012.12:g.56450132G>A
GRCh38.p14 chr 12 NC_000012.12:g.56450132G>T
GRCh37.p13 chr 12 NC_000012.11:g.56843916G>A
GRCh37.p13 chr 12 NC_000012.11:g.56843916G>T
MIP RefSeqGene (LRG_1291) NG_021397.2:g.24035C>T
MIP RefSeqGene (LRG_1291) NG_021397.2:g.24035C>A
Gene: MIP, major intrinsic protein of lens fiber (minus strand)
Molecule type Change Amino acid[Codon] SO Term
MIP transcript NM_012064.4:c.*1148= N/A 3 Prime UTR Variant
MIP transcript variant X1 XM_011538354.2:c.*1148= N/A 3 Prime UTR Variant
MIP transcript variant X2 XM_017019306.2:c.*1148= N/A 3 Prime UTR Variant
Gene: TIMELESS, timeless circadian regulator (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
TIMELESS transcript variant 2 NM_001330295.2:c. N/A Upstream Transcript Variant
TIMELESS transcript variant 1 NM_003920.5:c. N/A Upstream Transcript Variant
TIMELESS transcript variant 3 NR_138471.2:n. N/A Upstream 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
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 G= A T
GRCh38.p14 chr 12 NC_000012.12:g.56450132= NC_000012.12:g.56450132G>A NC_000012.12:g.56450132G>T
GRCh37.p13 chr 12 NC_000012.11:g.56843916= NC_000012.11:g.56843916G>A NC_000012.11:g.56843916G>T
MIP RefSeqGene (LRG_1291) NG_021397.2:g.24035= NG_021397.2:g.24035C>T NG_021397.2:g.24035C>A
MIP transcript NM_012064.4:c.*1148= NM_012064.4:c.*1148C>T NM_012064.4:c.*1148C>A
MIP transcript NM_012064.3:c.*1148= NM_012064.3:c.*1148C>T NM_012064.3:c.*1148C>A
MIP transcript variant X1 XM_011538354.2:c.*1148= XM_011538354.2:c.*1148C>T XM_011538354.2:c.*1148C>A
MIP transcript variant X1 XM_011538354.1:c.*1148= XM_011538354.1:c.*1148C>T XM_011538354.1:c.*1148C>A
MIP transcript variant X2 XM_017019306.2:c.*1148= XM_017019306.2:c.*1148C>T XM_017019306.2:c.*1148C>A
MIP transcript variant X2 XM_017019306.1:c.*1148= XM_017019306.1:c.*1148C>T XM_017019306.1:c.*1148C>A
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, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2875453 Jan 12, 2001 (92)
2 ABI ss38902679 Mar 14, 2006 (126)
3 HUMAN_LONGEVITY ss2190061338 Dec 20, 2016 (150)
4 GNOMAD ss4252402074 Apr 26, 2021 (155)
5 TOPMED ss4919478703 Apr 26, 2021 (155)
6 TOPMED ss4919478704 Apr 26, 2021 (155)
7 TOMMO_GENOMICS ss5756323125 Oct 16, 2022 (156)
8 gnomAD - Genomes NC_000012.12 - 56450132 Apr 26, 2021 (155)
9 HapMap NC_000012.12 - 56450132 Apr 27, 2020 (154)
10 14KJPN NC_000012.12 - 56450132 Oct 16, 2022 (156)
11 TopMed

Submission ignored due to conflicting rows:
Row 135024360 (NC_000012.12:56450131:G:A 9/264690)
Row 135024361 (NC_000012.12:56450131:G:T 16/264690)

- Apr 26, 2021 (155)
12 TopMed

Submission ignored due to conflicting rows:
Row 135024360 (NC_000012.12:56450131:G:A 9/264690)
Row 135024361 (NC_000012.12:56450131:G:T 16/264690)

- Apr 26, 2021 (155)
13 ALFA NC_000012.12 - 56450132 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
90160229, 5572710480, ss4919478703, ss5756323125 NC_000012.12:56450131:G:A NC_000012.12:56450131:G:A (self)
408339018, 822754, 5572710480, ss2190061338, ss4252402074, ss4919478704 NC_000012.12:56450131:G:T NC_000012.12:56450131:G:T (self)
ss2875453, ss38902679 NT_029419.12:18987221:G:T NC_000012.12:56450131:G:T (self)
Removed from this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Destination RSIDs
ss2354007152 NC_000012.11:56843915:G:A NC_000012.12:56450131:G:A
ss2354007153 NC_000012.11:56843915:G:T NC_000012.12:56450131:G:T
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 rs1971280

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