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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.

rs1491294179

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:233339379-233339380 (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
delTT
Variation Type
Deletion
Frequency
delTT=0.00324 (278/85854, GnomAD)
delTT=0.00382 (86/22514, 14KJPN)
delTT=0.00621 (98/15790, 8.3KJPN) (+ 2 more)
delTT=0.0084 (15/1784, Korea1K)
delTT=0.008 (5/594, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MAP3K21 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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 85854 TT=0.99676 delTT=0.00324
gnomAD - Genomes European Sub 51576 TT=0.99589 delTT=0.00411
gnomAD - Genomes African Sub 22582 TT=0.99903 delTT=0.00097
gnomAD - Genomes American Sub 6342 TT=0.9970 delTT=0.0030
gnomAD - Genomes Ashkenazi Jewish Sub 2488 TT=0.9932 delTT=0.0068
gnomAD - Genomes East Asian Sub 1618 TT=0.9969 delTT=0.0031
gnomAD - Genomes Other Sub 1248 TT=0.9976 delTT=0.0024
14KJPN JAPANESE Study-wide 22514 TT=0.99618 delTT=0.00382
8.3KJPN JAPANESE Study-wide 15790 TT=0.99379 delTT=0.00621
Korean Genome Project KOREAN Study-wide 1784 TT=0.9916 delTT=0.0084
Northern Sweden ACPOP Study-wide 594 TT=0.992 delTT=0.008
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 1 NC_000001.11:g.233339379_233339380del
GRCh37.p13 chr 1 NC_000001.10:g.233475125_233475126del
Gene: MAP3K21, mitogen-activated protein kinase kinase kinase 21 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MAP3K21 transcript NM_032435.3:c.806-7063_80…

NM_032435.3:c.806-7063_806-7062del

N/A Intron 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 TT= delTT
GRCh38.p14 chr 1 NC_000001.11:g.233339379_233339380= NC_000001.11:g.233339379_233339380del
GRCh37.p13 chr 1 NC_000001.10:g.233475125_233475126= NC_000001.10:g.233475125_233475126del
MAP3K21 transcript NM_032435.2:c.806-7063= NM_032435.2:c.806-7063_806-7062del
MAP3K21 transcript NM_032435.3:c.806-7063= NM_032435.3:c.806-7063_806-7062del
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#.

9 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2767518173 Jan 10, 2018 (151)
2 ACPOP ss3727963060 Jul 12, 2019 (153)
3 PACBIO ss3783718393 Jul 12, 2019 (153)
4 KOGIC ss3946731390 Apr 25, 2020 (154)
5 TOMMO_GENOMICS ss5148958987 Apr 25, 2021 (155)
6 1000G_HIGH_COVERAGE ss5246197245 Oct 12, 2022 (156)
7 HUGCELL_USP ss5446593783 Oct 12, 2022 (156)
8 SANFORD_IMAGENETICS ss5627675397 Oct 12, 2022 (156)
9 TOMMO_GENOMICS ss5676871654 Oct 12, 2022 (156)
10 gnomAD - Genomes NC_000001.11 - 233339379 Apr 25, 2021 (155)
11 Korean Genome Project NC_000001.11 - 233339379 Apr 25, 2020 (154)
12 Northern Sweden NC_000001.10 - 233475125 Jul 12, 2019 (153)
13 8.3KJPN NC_000001.10 - 233475125 Apr 25, 2021 (155)
14 14KJPN NC_000001.11 - 233339379 Oct 12, 2022 (156)
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
1247925, 6928294, ss2767518173, ss3727963060, ss3783718393, ss5148958987, ss5627675397 NC_000001.10:233475124:TT: NC_000001.11:233339378:TT: (self)
42886879, 3109391, 10708758, ss3946731390, ss5246197245, ss5446593783, ss5676871654 NC_000001.11:233339378:TT: NC_000001.11:233339378:TT: (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 rs1491294179

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