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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.

rs1472505549

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr7:32070319 (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
delC
Variation Type
Deletion
Frequency
delC=0.000011 (3/264690, TOPMED)
delC=0.000004 (1/251468, GnomAD_exome)
delC=0.00009 (1/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PDE1C : 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 10680 C=0.99991 =0.00009 0.999813 0.0 0.000187 0
European Sub 6962 C=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Sub 2294 C=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 C=1.00 =0.00 1.0 0.0 0.0 N/A
African American Sub 2210 C=1.0000 =0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 C=1.000 =0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 C=1.00 =0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 C=1.00 =0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 C=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 C=0.998 =0.002 0.996721 0.0 0.003279 0
South Asian Sub 94 C=1.00 =0.00 1.0 0.0 0.0 N/A
Other Sub 466 C=1.000 =0.000 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 264690 C=0.999989 delC=0.000011
gnomAD - Exomes Global Study-wide 251468 C=0.999996 delC=0.000004
gnomAD - Exomes European Sub 135414 C=1.000000 delC=0.000000
gnomAD - Exomes Asian Sub 49008 C=1.00000 delC=0.00000
gnomAD - Exomes American Sub 34574 C=0.99997 delC=0.00003
gnomAD - Exomes African Sub 16256 C=1.00000 delC=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10080 C=1.00000 delC=0.00000
gnomAD - Exomes Other Sub 6136 C=1.0000 delC=0.0000
Allele Frequency Aggregator Total Global 10680 C=0.99991 delC=0.00009
Allele Frequency Aggregator European Sub 6962 C=1.0000 delC=0.0000
Allele Frequency Aggregator African Sub 2294 C=1.0000 delC=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 C=0.998 delC=0.002
Allele Frequency Aggregator Other Sub 466 C=1.000 delC=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 C=1.000 delC=0.000
Allele Frequency Aggregator Asian Sub 108 C=1.000 delC=0.000
Allele Frequency Aggregator South Asian Sub 94 C=1.00 delC=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 7 NC_000007.14:g.32070319del
GRCh37.p13 chr 7 NC_000007.13:g.32109931del
PDE1C RefSeqGene NG_051183.1:g.362906del
Gene: PDE1C, phosphodiesterase 1C (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PDE1C transcript variant 3 NM_001191058.4:c.308+9946…

NM_001191058.4:c.308+99466del

N/A Intron Variant
PDE1C transcript variant 9 NM_001322058.2:c.308+9946…

NM_001322058.2:c.308+99466del

N/A Intron Variant
PDE1C transcript variant 10 NM_001322059.2:c.533+9946…

NM_001322059.2:c.533+99466del

N/A Intron Variant
PDE1C transcript variant 1 NM_001191056.3:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 1 NP_001177985.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant 2 NM_001191057.4:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 2 NP_001177986.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant 4 NM_005020.5:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 1 NP_005011.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant 6 NM_001322055.2:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 2 NP_001308984.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant 7 NM_001322056.2:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 1 NP_001308985.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant 5 NM_001191059.4:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 2 NP_001177988.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant 8 NM_001322057.2:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 1 NP_001308986.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant X1 XM_017012264.1:c.413+9946…

XM_017012264.1:c.413+99466del

N/A Intron Variant
PDE1C transcript variant X4 XM_017012265.1:c.248+9946…

XM_017012265.1:c.248+99466del

N/A Intron Variant
PDE1C transcript variant X5 XM_017012266.2:c.413+9946…

XM_017012266.2:c.413+99466del

N/A Intron Variant
PDE1C transcript variant X16 XM_047420445.1:c. N/A Genic Upstream Transcript Variant
PDE1C transcript variant X17 XM_047420446.1:c. N/A Genic Upstream Transcript Variant
PDE1C transcript variant X6 XM_047420440.1:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform X4 XP_047276396.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant X7 XM_017012267.2:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform X4 XP_016867756.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant X9 XM_047420441.1:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform X5 XP_047276397.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant X11 XM_047420442.1:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform X5 XP_047276398.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant X12 XM_047420443.1:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform X5 XP_047276399.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant X15 XM_047420444.1:c.75del E [GAG] > E [GA] Coding Sequence Variant
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform X6 XP_047276400.1:p.Ile27fs E (Glu) > E (Glu) Frameshift Variant
PDE1C transcript variant X10 XR_007060042.1:n.127del N/A Non Coding Transcript Variant
PDE1C transcript variant X13 XR_007060043.1:n.544del N/A Non Coding Transcript Variant
PDE1C transcript variant X14 XR_007060044.1:n.127del N/A Non Coding Transcript Variant
PDE1C transcript variant X2 XR_001744802.1:n. N/A Intron Variant
PDE1C transcript variant X3 XR_001744803.1:n. N/A Intron Variant
PDE1C transcript variant X8 XR_007060041.1:n. 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 C= delC
GRCh38.p14 chr 7 NC_000007.14:g.32070319= NC_000007.14:g.32070319del
GRCh37.p13 chr 7 NC_000007.13:g.32109931= NC_000007.13:g.32109931del
PDE1C RefSeqGene NG_051183.1:g.362906= NG_051183.1:g.362906del
PDE1C transcript variant 4 NM_005020.5:c.75= NM_005020.5:c.75del
PDE1C transcript variant 4 NM_005020.4:c.75= NM_005020.4:c.75del
PDE1C transcript variant 4 NM_005020.3:c.75= NM_005020.3:c.75del
PDE1C transcript variant 4 NM_005020.2:c.75= NM_005020.2:c.75del
PDE1C transcript variant 5 NM_001191059.4:c.75= NM_001191059.4:c.75del
PDE1C transcript variant 5 NM_001191059.3:c.75= NM_001191059.3:c.75del
PDE1C transcript variant 5 NM_001191059.2:c.75= NM_001191059.2:c.75del
PDE1C transcript variant 5 NM_001191059.1:c.75= NM_001191059.1:c.75del
PDE1C transcript variant 2 NM_001191057.4:c.75= NM_001191057.4:c.75del
PDE1C transcript variant 2 NM_001191057.3:c.75= NM_001191057.3:c.75del
PDE1C transcript variant 2 NM_001191057.2:c.75= NM_001191057.2:c.75del
PDE1C transcript variant 2 NM_001191057.1:c.75= NM_001191057.1:c.75del
PDE1C transcript variant 1 NM_001191056.3:c.75= NM_001191056.3:c.75del
PDE1C transcript variant 1 NM_001191056.2:c.75= NM_001191056.2:c.75del
PDE1C transcript variant 1 NM_001191056.1:c.75= NM_001191056.1:c.75del
PDE1C transcript variant 8 NM_001322057.2:c.75= NM_001322057.2:c.75del
PDE1C transcript variant 8 NM_001322057.1:c.75= NM_001322057.1:c.75del
PDE1C transcript variant 7 NM_001322056.2:c.75= NM_001322056.2:c.75del
PDE1C transcript variant 7 NM_001322056.1:c.75= NM_001322056.1:c.75del
PDE1C transcript variant 6 NM_001322055.2:c.75= NM_001322055.2:c.75del
PDE1C transcript variant 6 NM_001322055.1:c.75= NM_001322055.1:c.75del
PDE1C transcript variant X7 XM_017012267.2:c.75= XM_017012267.2:c.75del
PDE1C transcript variant X6 XM_017012267.1:c.75= XM_017012267.1:c.75del
PDE1C transcript variant X15 XM_047420444.1:c.75= XM_047420444.1:c.75del
PDE1C transcript variant X6 XM_047420440.1:c.75= XM_047420440.1:c.75del
PDE1C transcript variant X13 XR_007060043.1:n.544= XR_007060043.1:n.544del
PDE1C transcript variant X9 XM_047420441.1:c.75= XM_047420441.1:c.75del
PDE1C transcript variant X12 XM_047420443.1:c.75= XM_047420443.1:c.75del
PDE1C transcript variant X11 XM_047420442.1:c.75= XM_047420442.1:c.75del
PDE1C transcript variant X10 XR_007060042.1:n.127= XR_007060042.1:n.127del
PDE1C transcript variant X14 XR_007060044.1:n.127= XR_007060044.1:n.127del
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 1 NP_005011.1:p.Glu25= NP_005011.1:p.Ile27fs
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 2 NP_001177988.1:p.Glu25= NP_001177988.1:p.Ile27fs
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 2 NP_001177986.1:p.Glu25= NP_001177986.1:p.Ile27fs
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 1 NP_001177985.1:p.Glu25= NP_001177985.1:p.Ile27fs
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 1 NP_001308986.1:p.Glu25= NP_001308986.1:p.Ile27fs
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 1 NP_001308985.1:p.Glu25= NP_001308985.1:p.Ile27fs
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform 2 NP_001308984.1:p.Glu25= NP_001308984.1:p.Ile27fs
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform X4 XP_016867756.1:p.Glu25= XP_016867756.1:p.Ile27fs
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform X6 XP_047276400.1:p.Glu25= XP_047276400.1:p.Ile27fs
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform X4 XP_047276396.1:p.Glu25= XP_047276396.1:p.Ile27fs
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform X5 XP_047276397.1:p.Glu25= XP_047276397.1:p.Ile27fs
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform X5 XP_047276399.1:p.Glu25= XP_047276399.1:p.Ile27fs
dual specificity calcium/calmodulin-dependent 3',5'-cyclic nucleotide phosphodiesterase 1C isoform X5 XP_047276398.1:p.Glu25= XP_047276398.1:p.Ile27fs
PDE1C transcript variant 3 NM_001191058.1:c.308+99466= NM_001191058.1:c.308+99466del
PDE1C transcript variant 3 NM_001191058.4:c.308+99466= NM_001191058.4:c.308+99466del
PDE1C transcript variant 9 NM_001322058.2:c.308+99466= NM_001322058.2:c.308+99466del
PDE1C transcript variant 10 NM_001322059.2:c.533+99466= NM_001322059.2:c.533+99466del
PDE1C transcript variant X1 XM_005249766.1:c.131+7551= XM_005249766.1:c.131+7551del
PDE1C transcript variant X3 XM_005249768.1:c.308+99466= XM_005249768.1:c.308+99466del
PDE1C transcript variant X1 XM_017012264.1:c.413+99466= XM_017012264.1:c.413+99466del
PDE1C transcript variant X4 XM_017012265.1:c.248+99466= XM_017012265.1:c.248+99466del
PDE1C transcript variant X5 XM_017012266.2:c.413+99466= XM_017012266.2:c.413+99466del
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, 3 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2736369716 Nov 08, 2017 (151)
2 TOPMED ss4740942893 Apr 26, 2021 (155)
3 gnomAD - Exomes NC_000007.13 - 32109931 Jul 13, 2019 (153)
4 TopMed NC_000007.14 - 32070319 Apr 26, 2021 (155)
5 ALFA NC_000007.14 - 32070319 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
5529960, ss2736369716 NC_000007.13:32109930:C: NC_000007.14:32070318:C: (self)
578320452, 540419508, ss4740942893 NC_000007.14:32070318:C: NC_000007.14:32070318: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 rs1472505549

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