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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.

rs1491450846

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:179681944-179681945 (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
delTA
Variation Type
Deletion
Frequency
delTA=0.000239 (27/112822, GnomAD)
delTA=0.00017 (2/11862, ALFA)
delTA=0.0002 (1/6404, 1000G_30x)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CANX : Intron Variant
CBY3 : 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 11862 TA=0.99983 =0.00017 0.999663 0.0 0.000337 0
European Sub 7618 TA=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Sub 2816 TA=0.9996 =0.0004 0.99929 0.0 0.00071 0
African Others Sub 108 TA=1.000 =0.000 1.0 0.0 0.0 N/A
African American Sub 2708 TA=0.9996 =0.0004 0.999261 0.0 0.000739 0
Asian Sub 108 TA=1.000 =0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 TA=1.00 =0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 TA=1.00 =0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 TA=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 TA=1.000 =0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 TA=1.00 =0.00 1.0 0.0 0.0 N/A
Other Sub 470 TA=0.998 =0.002 0.995745 0.0 0.004255 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 - Genomes Global Study-wide 112822 TA=0.999761 delTA=0.000239
gnomAD - Genomes European Sub 61542 TA=1.00000 delTA=0.00000
gnomAD - Genomes African Sub 33868 TA=0.99923 delTA=0.00077
gnomAD - Genomes American Sub 10374 TA=0.99990 delTA=0.00010
gnomAD - Genomes Ashkenazi Jewish Sub 2874 TA=1.0000 delTA=0.0000
gnomAD - Genomes East Asian Sub 2474 TA=1.0000 delTA=0.0000
gnomAD - Genomes Other Sub 1690 TA=1.0000 delTA=0.0000
Allele Frequency Aggregator Total Global 11862 TA=0.99983 delTA=0.00017
Allele Frequency Aggregator European Sub 7618 TA=1.0000 delTA=0.0000
Allele Frequency Aggregator African Sub 2816 TA=0.9996 delTA=0.0004
Allele Frequency Aggregator Latin American 2 Sub 610 TA=1.000 delTA=0.000
Allele Frequency Aggregator Other Sub 470 TA=0.998 delTA=0.002
Allele Frequency Aggregator Latin American 1 Sub 146 TA=1.000 delTA=0.000
Allele Frequency Aggregator Asian Sub 108 TA=1.000 delTA=0.000
Allele Frequency Aggregator South Asian Sub 94 TA=1.00 delTA=0.00
1000Genomes_30x Global Study-wide 6404 TA=0.9998 delTA=0.0002
1000Genomes_30x African Sub 1786 TA=0.9994 delTA=0.0006
1000Genomes_30x Europe Sub 1266 TA=1.0000 delTA=0.0000
1000Genomes_30x South Asian Sub 1202 TA=1.0000 delTA=0.0000
1000Genomes_30x East Asian Sub 1170 TA=1.0000 delTA=0.0000
1000Genomes_30x American Sub 980 TA=1.000 delTA=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 5 NC_000005.10:g.179681944_179681945del
GRCh37.p13 chr 5 NC_000005.9:g.179108945_179108946del
GRCh38.p14 chr 5 fix patch HG30_PATCH NW_016107298.1:g.447636_447637del
Gene: CANX, calnexin (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CANX transcript variant 2 NM_001024649.2:c. N/A Genic Upstream Transcript Variant
CANX transcript variant 3 NM_001363993.1:c. N/A Genic Upstream Transcript Variant
CANX transcript variant 4 NM_001363994.1:c. N/A Genic Upstream Transcript Variant
CANX transcript variant 5 NM_001363995.1:c. N/A Genic Upstream Transcript Variant
CANX transcript variant 6 NM_001363996.1:c. N/A Genic Upstream Transcript Variant
CANX transcript variant 7 NM_001363997.1:c. N/A Genic Upstream Transcript Variant
CANX transcript variant 8 NM_001363998.1:c. N/A Genic Upstream Transcript Variant
CANX transcript variant 9 NM_001363999.1:c. N/A Genic Upstream Transcript Variant
CANX transcript variant 10 NM_001364000.1:c. N/A Genic Upstream Transcript Variant
CANX transcript variant 11 NM_001364001.1:c. N/A Genic Upstream Transcript Variant
CANX transcript variant 1 NM_001746.4:c. N/A Genic Upstream Transcript Variant
CANX transcript variant 12 NR_157048.1:n. N/A Genic Upstream Transcript Variant
CANX transcript variant X1 XM_011534665.4:c.-4+3167_…

XM_011534665.4:c.-4+3167_-4+3168del

N/A Intron Variant
CANX transcript variant X2 XM_047417792.1:c. N/A Genic Upstream Transcript Variant
Gene: CBY3, chibby family member 3 (minus strand) : 2KB Upstream Variant
Molecule type Change Amino acid[Codon] SO Term
CBY3 transcript NM_001164444.2:c. N/A Upstream Transcript Variant
CBY3 transcript variant X1 XM_047417524.1:c. 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 TA= delTA
GRCh38.p14 chr 5 NC_000005.10:g.179681944_179681945= NC_000005.10:g.179681944_179681945del
GRCh37.p13 chr 5 NC_000005.9:g.179108945_179108946= NC_000005.9:g.179108945_179108946del
GRCh38.p14 chr 5 fix patch HG30_PATCH NW_016107298.1:g.447636_447637= NW_016107298.1:g.447636_447637del
CANX transcript variant X1 XM_011534665.4:c.-4+3167= XM_011534665.4:c.-4+3167_-4+3168del
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#.

4 SubSNP, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2834689538 Jan 10, 2018 (151)
2 HUGCELL_USP ss5464881702 Oct 13, 2022 (156)
3 1000G_HIGH_COVERAGE ss5552312296 Oct 13, 2022 (156)
4 SANFORD_IMAGENETICS ss5639566948 Oct 13, 2022 (156)
5 1000Genomes_30x NC_000005.10 - 179681944 Oct 13, 2022 (156)
6 gnomAD - Genomes NC_000005.10 - 179681944 Apr 26, 2021 (155)
7 ALFA NC_000005.10 - 179681944 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
ss2834689538, ss5639566948 NC_000005.9:179108944:TA: NC_000005.10:179681943:TA: (self)
39838231, 214324995, 8617528530, ss5464881702, ss5552312296 NC_000005.10:179681943:TA: NC_000005.10:179681943:TA: (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 rs1491450846

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