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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs1490878513

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr2:240561446 (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
A>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000004 (1/250138, GnomAD_exome)
C=0.0001 (1/8988, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
DUSP28 : Missense Variant
ANKMY1 : 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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 8988 A=0.9999 C=0.0001 0.999777 0.0 0.000223 0
European Sub 6062 A=1.0000 C=0.0000 1.0 0.0 0.0 N/A
African Sub 594 A=1.000 C=0.000 1.0 0.0 0.0 N/A
African Others Sub 8 A=1.0 C=0.0 1.0 0.0 0.0 N/A
African American Sub 586 A=1.000 C=0.000 1.0 0.0 0.0 N/A
Asian Sub 56 A=1.00 C=0.00 1.0 0.0 0.0 N/A
East Asian Sub 26 A=1.00 C=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 30 A=1.00 C=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 0 A=0 C=0 0 0 0 N/A
Latin American 2 Sub 0 A=0 C=0 0 0 0 N/A
South Asian Sub 0 A=0 C=0 0 0 0 N/A
Other Sub 2276 A=0.9996 C=0.0004 0.999121 0.0 0.000879 0


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 250138 A=0.999996 C=0.000004
gnomAD - Exomes European Sub 134492 A=0.999993 C=0.000007
gnomAD - Exomes Asian Sub 48962 A=1.00000 C=0.00000
gnomAD - Exomes American Sub 34540 A=1.00000 C=0.00000
gnomAD - Exomes African Sub 15996 A=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10044 A=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6104 A=1.0000 C=0.0000
Allele Frequency Aggregator Total Global 8988 A=0.9999 C=0.0001
Allele Frequency Aggregator European Sub 6062 A=1.0000 C=0.0000
Allele Frequency Aggregator Other Sub 2276 A=0.9996 C=0.0004
Allele Frequency Aggregator African Sub 594 A=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 56 A=1.00 C=0.00
Allele Frequency Aggregator Latin American 1 Sub 0 A=0 C=0
Allele Frequency Aggregator Latin American 2 Sub 0 A=0 C=0
Allele Frequency Aggregator South Asian Sub 0 A=0 C=0
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 2 NC_000002.12:g.240561446A>C
GRCh37.p13 chr 2 NC_000002.11:g.241500863A>C
Gene: ANKMY1, ankyrin repeat and MYND domain containing 1 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
ANKMY1 transcript variant 6 NM_001308375.4:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 10 NM_001354023.3:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 7 NM_001354024.3:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 9 NM_001354026.3:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 14 NM_001393462.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 15 NM_001393463.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 16 NM_001393464.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 17 NM_001393465.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 18 NM_001393466.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 19 NM_001393467.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 20 NM_001393468.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 21 NM_001393469.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 22 NM_001393470.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 23 NM_001393471.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 24 NM_001393472.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 26 NM_001393474.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 27 NM_001393475.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 28 NM_001393476.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 29 NM_001393477.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 30 NM_001393478.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 31 NM_001393479.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 33 NM_001393481.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 34 NM_001393482.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 35 NM_001393483.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 36 NM_001393484.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 37 NM_001393485.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant 3 NM_001282771.3:c. N/A N/A
ANKMY1 transcript variant 4 NM_001282780.2:c. N/A N/A
ANKMY1 transcript variant 5 NM_001282781.2:c. N/A N/A
ANKMY1 transcript variant 25 NM_001393473.1:c. N/A N/A
ANKMY1 transcript variant 32 NM_001393480.1:c. N/A N/A
ANKMY1 transcript variant 1 NM_016552.5:c. N/A N/A
ANKMY1 transcript variant 2 NM_017844.4:c. N/A N/A
ANKMY1 transcript variant 11 NR_148696.3:n. N/A Upstream Transcript Variant
ANKMY1 transcript variant 12 NR_148697.3:n. N/A Upstream Transcript Variant
ANKMY1 transcript variant 13 NR_148698.2:n. N/A Upstream Transcript Variant
ANKMY1 transcript variant 8 NR_171690.1:n. N/A Upstream Transcript Variant
ANKMY1 transcript variant 38 NR_171691.1:n. N/A Upstream Transcript Variant
ANKMY1 transcript variant 39 NR_171692.1:n. N/A Upstream Transcript Variant
ANKMY1 transcript variant 40 NR_171693.1:n. N/A Upstream Transcript Variant
ANKMY1 transcript variant 41 NR_171694.1:n. N/A Upstream Transcript Variant
ANKMY1 transcript variant 42 NR_171695.1:n. N/A Upstream Transcript Variant
ANKMY1 transcript variant 43 NR_171696.1:n. N/A Upstream Transcript Variant
ANKMY1 transcript variant 44 NR_171697.1:n. N/A Upstream Transcript Variant
ANKMY1 transcript variant 45 NR_171698.1:n. N/A Upstream Transcript Variant
ANKMY1 transcript variant X1 XM_047444649.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X2 XM_047444650.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X3 XM_047444651.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X4 XM_047444652.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X5 XM_047444653.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X6 XM_047444654.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X7 XM_047444655.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X8 XM_047444656.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X9 XM_047444657.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X10 XM_047444658.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X11 XM_047444659.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X12 XM_047444660.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X13 XM_047444661.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X14 XM_047444662.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X15 XM_047444663.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X16 XM_047444664.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X17 XM_047444665.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X18 XM_047444666.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X19 XM_047444667.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X20 XM_047444668.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X21 XM_047444669.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X22 XM_047444670.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X23 XM_047444671.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X24 XM_047444672.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X25 XM_047444673.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X26 XM_047444674.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X27 XM_047444675.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X29 XM_047444677.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X30 XM_047444678.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X31 XM_047444679.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X33 XM_047444681.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X35 XM_047444682.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X36 XM_047444683.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X37 XM_047444684.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X38 XM_047444685.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X39 XM_047444686.1:c. N/A Upstream Transcript Variant
ANKMY1 transcript variant X28 XM_047444676.1:c. N/A N/A
ANKMY1 transcript variant X32 XM_047444680.1:c. N/A N/A
ANKMY1 transcript variant X34 XR_007076387.1:n. N/A Upstream Transcript Variant
Gene: DUSP28, dual specificity phosphatase 28 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
DUSP28 transcript variant 2 NM_001033575.1:c.510A>C L [TTA] > F [TTC] Coding Sequence Variant
dual specificity phosphatase 28 NP_001028747.1:p.Leu170Phe L (Leu) > F (Phe) Missense Variant
DUSP28 transcript variant 1 NM_001370465.2:c.510A>C L [TTA] > F [TTC] Coding Sequence Variant
dual specificity phosphatase 28 NP_001357394.1:p.Leu170Phe L (Leu) > F (Phe) Missense 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 A= C
GRCh38.p14 chr 2 NC_000002.12:g.240561446= NC_000002.12:g.240561446A>C
GRCh37.p13 chr 2 NC_000002.11:g.241500863= NC_000002.11:g.241500863A>C
DUSP28 transcript variant 1 NM_001370465.2:c.510= NM_001370465.2:c.510A>C
DUSP28 transcript variant 1 NM_001370465.1:c.510= NM_001370465.1:c.510A>C
DUSP28 transcript variant 2 NM_001033575.1:c.510= NM_001033575.1:c.510A>C
dual specificity phosphatase 28 NP_001357394.1:p.Leu170= NP_001357394.1:p.Leu170Phe
dual specificity phosphatase 28 NP_001028747.1:p.Leu170= NP_001028747.1:p.Leu170Phe
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#.

1 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2733469273 Nov 08, 2017 (151)
2 gnomAD - Exomes NC_000002.11 - 241500863 Jul 13, 2019 (153)
3 ALFA NC_000002.12 - 240561446 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
2538892, ss2733469273 NC_000002.11:241500862:A:C NC_000002.12:240561445:A:C (self)
12008746427 NC_000002.12:240561445:A:C NC_000002.12:240561445:A:C (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 rs1490878513

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