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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.

rs1406807584

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr21:46644475 (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
dupG
Variation Type
Indel Insertion and Deletion
Frequency
dupG=0.00000 (0/71810, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRMT2 : Frameshift 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 71810 G=1.00000 GG=0.00000 1.0 0.0 0.0 N/A
European Sub 65830 G=1.00000 GG=0.00000 1.0 0.0 0.0 N/A
African Sub 800 G=1.000 GG=0.000 1.0 0.0 0.0 N/A
African Others Sub 52 G=1.00 GG=0.00 1.0 0.0 0.0 N/A
African American Sub 748 G=1.000 GG=0.000 1.0 0.0 0.0 N/A
Asian Sub 3162 G=1.0000 GG=0.0000 1.0 0.0 0.0 N/A
East Asian Sub 2562 G=1.0000 GG=0.0000 1.0 0.0 0.0 N/A
Other Asian Sub 600 G=1.000 GG=0.000 1.0 0.0 0.0 N/A
Latin American 1 Sub 290 G=1.000 GG=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 318 G=1.000 GG=0.000 1.0 0.0 0.0 N/A
South Asian Sub 176 G=1.000 GG=0.000 1.0 0.0 0.0 N/A
Other Sub 1234 G=1.0000 GG=0.0000 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").

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Study Population Group Sample Size Ref Allele Alt Allele
Allele Frequency Aggregator Total Global 71810 G=1.00000 dupG=0.00000
Allele Frequency Aggregator European Sub 65830 G=1.00000 dupG=0.00000
Allele Frequency Aggregator Asian Sub 3162 G=1.0000 dupG=0.0000
Allele Frequency Aggregator Other Sub 1234 G=1.0000 dupG=0.0000
Allele Frequency Aggregator African Sub 800 G=1.000 dupG=0.000
Allele Frequency Aggregator Latin American 2 Sub 318 G=1.000 dupG=0.000
Allele Frequency Aggregator Latin American 1 Sub 290 G=1.000 dupG=0.000
Allele Frequency Aggregator South Asian Sub 176 G=1.000 dupG=0.000
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 21 NC_000021.9:g.46644475dup
GRCh37.p13 chr 21 NC_000021.8:g.48064387dup
Gene: PRMT2, protein arginine methyltransferase 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PRMT2 transcript variant 1 NM_206962.4:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform 1 NP_996845.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant 5 NM_001242866.3:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform 4 NP_001229795.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant 2 NM_001535.5:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform 1 NP_001526.2:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant 4 NM_001242865.3:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform 3 NP_001229794.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant 8 NM_001286678.2:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform 7 NP_001273607.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant 7 NM_001286677.2:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform 6 NP_001273606.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant 3 NM_001242864.3:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform 2 NP_001229793.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant 6 NM_001286676.2:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform 5 NP_001273605.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant X1 XM_005261111.5:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform X1 XP_005261168.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant X2 XM_006723998.5:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform X2 XP_006724061.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant X3 XM_047440759.1:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform X2 XP_047296715.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant X4 XM_006723999.4:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform X3 XP_006724062.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant X5 XM_047440760.1:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform X3 XP_047296716.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant X6 XM_047440761.1:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform X3 XP_047296717.1:p.Ser105fs S (Ser) > R (Arg) Frameshift Variant
PRMT2 transcript variant X7 XM_006724000.4:c.314dup S [AGC] > R [AGGC] Coding Sequence Variant
protein arginine N-methyltransferase 2 isoform X4 XP_006724063.1:p.Ser105fs S (Ser) > R (Arg) Frameshift 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= dupG
GRCh38.p14 chr 21 NC_000021.9:g.46644475= NC_000021.9:g.46644475dup
GRCh37.p13 chr 21 NC_000021.8:g.48064387= NC_000021.8:g.48064387dup
PRMT2 transcript variant X1 XM_005261111.5:c.314= XM_005261111.5:c.314dup
PRMT2 transcript variant X1 XM_005261111.4:c.314= XM_005261111.4:c.314dup
PRMT2 transcript variant X1 XM_005261111.3:c.314= XM_005261111.3:c.314dup
PRMT2 transcript variant X1 XM_005261111.2:c.314= XM_005261111.2:c.314dup
PRMT2 transcript variant X1 XM_005261111.1:c.314= XM_005261111.1:c.314dup
PRMT2 transcript variant 2 NM_001535.5:c.314= NM_001535.5:c.314dup
PRMT2 transcript variant 2 NM_001535.4:c.314= NM_001535.4:c.314dup
PRMT2 transcript variant 2 NM_001535.3:c.314= NM_001535.3:c.314dup
PRMT2 transcript variant X2 XM_006723998.5:c.314= XM_006723998.5:c.314dup
PRMT2 transcript variant X2 XM_006723998.4:c.314= XM_006723998.4:c.314dup
PRMT2 transcript variant X2 XM_006723998.3:c.314= XM_006723998.3:c.314dup
PRMT2 transcript variant X2 XM_006723998.2:c.314= XM_006723998.2:c.314dup
PRMT2 transcript variant X2 XM_006723998.1:c.314= XM_006723998.1:c.314dup
PRMT2 transcript variant 1 NM_206962.4:c.314= NM_206962.4:c.314dup
PRMT2 transcript variant 1 NM_206962.3:c.314= NM_206962.3:c.314dup
PRMT2 transcript variant 1 NM_206962.2:c.314= NM_206962.2:c.314dup
PRMT2 transcript variant X7 XM_006724000.4:c.314= XM_006724000.4:c.314dup
PRMT2 transcript variant X7 XM_006724000.3:c.314= XM_006724000.3:c.314dup
PRMT2 transcript variant X7 XM_006724000.2:c.314= XM_006724000.2:c.314dup
PRMT2 transcript variant X4 XM_006724000.1:c.314= XM_006724000.1:c.314dup
PRMT2 transcript variant X4 XM_006723999.4:c.314= XM_006723999.4:c.314dup
PRMT2 transcript variant X3 XM_006723999.3:c.314= XM_006723999.3:c.314dup
PRMT2 transcript variant X3 XM_006723999.2:c.314= XM_006723999.2:c.314dup
PRMT2 transcript variant X3 XM_006723999.1:c.314= XM_006723999.1:c.314dup
PRMT2 transcript variant 4 NM_001242865.3:c.314= NM_001242865.3:c.314dup
PRMT2 transcript variant 4 NM_001242865.2:c.314= NM_001242865.2:c.314dup
PRMT2 transcript variant 4 NM_001242865.1:c.314= NM_001242865.1:c.314dup
PRMT2 transcript variant 5 NM_001242866.3:c.314= NM_001242866.3:c.314dup
PRMT2 transcript variant 5 NM_001242866.2:c.314= NM_001242866.2:c.314dup
PRMT2 transcript variant 5 NM_001242866.1:c.314= NM_001242866.1:c.314dup
PRMT2 transcript variant 3 NM_001242864.3:c.314= NM_001242864.3:c.314dup
PRMT2 transcript variant 3 NM_001242864.2:c.314= NM_001242864.2:c.314dup
PRMT2 transcript variant 3 NM_001242864.1:c.314= NM_001242864.1:c.314dup
PRMT2 transcript variant 7 NM_001286677.2:c.314= NM_001286677.2:c.314dup
PRMT2 transcript variant 7 NM_001286677.1:c.314= NM_001286677.1:c.314dup
PRMT2 transcript variant 6 NM_001286676.2:c.314= NM_001286676.2:c.314dup
PRMT2 transcript variant 6 NM_001286676.1:c.314= NM_001286676.1:c.314dup
PRMT2 transcript variant 8 NM_001286678.2:c.314= NM_001286678.2:c.314dup
PRMT2 transcript variant 8 NM_001286678.1:c.314= NM_001286678.1:c.314dup
PRMT2 transcript variant X3 XM_047440759.1:c.314= XM_047440759.1:c.314dup
PRMT2 transcript variant X6 XM_047440761.1:c.314= XM_047440761.1:c.314dup
PRMT2 transcript variant X5 XM_047440760.1:c.314= XM_047440760.1:c.314dup
protein arginine N-methyltransferase 2 isoform X1 XP_005261168.1:p.Ser105= XP_005261168.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform 1 NP_001526.2:p.Ser105= NP_001526.2:p.Ser105fs
protein arginine N-methyltransferase 2 isoform X2 XP_006724061.1:p.Ser105= XP_006724061.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform 1 NP_996845.1:p.Ser105= NP_996845.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform X4 XP_006724063.1:p.Ser105= XP_006724063.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform X3 XP_006724062.1:p.Ser105= XP_006724062.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform 3 NP_001229794.1:p.Ser105= NP_001229794.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform 4 NP_001229795.1:p.Ser105= NP_001229795.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform 2 NP_001229793.1:p.Ser105= NP_001229793.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform 6 NP_001273606.1:p.Ser105= NP_001273606.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform 5 NP_001273605.1:p.Ser105= NP_001273605.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform 7 NP_001273607.1:p.Ser105= NP_001273607.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform X2 XP_047296715.1:p.Ser105= XP_047296715.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform X3 XP_047296717.1:p.Ser105= XP_047296717.1:p.Ser105fs
protein arginine N-methyltransferase 2 isoform X3 XP_047296716.1:p.Ser105= XP_047296716.1:p.Ser105fs
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#.

2 SubSNP, 1 Frequency submissions
No Submitter Submission ID Date (Build)
1 AFFY ss2985232172 Nov 08, 2017 (151)
2 ILLUMINA ss3654000159 Oct 12, 2018 (152)
3 ALFA NC_000021.9 - 46644475 Apr 27, 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
ss2985232172, ss3654000159 NC_000021.8:48064386::G NC_000021.9:46644474:G:GG (self)
2641326298 NC_000021.9:46644474:G:GG NC_000021.9:46644474:G:GG (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 rs1406807584

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