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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr4:165379308 (GRCh38.p13) 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.

G>A / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
C=0.000007 (1/147390, GnomAD_exome)
A=0.000014 (2/139982, GnomAD)
A=0.00000 (0/14050, ALFA) (+ 3 more)
C=0.00000 (0/14050, ALFA)
T=0.00000 (0/14050, ALFA)
C=0.00008 (1/12652, ExAC)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CPE : Missense Variant
0 citations
Genomic View
See rs on genome

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.p13 chr 4 NC_000004.12:g.165379308G>A
GRCh38.p13 chr 4 NC_000004.12:g.165379308G>C
GRCh38.p13 chr 4 NC_000004.12:g.165379308G>T
GRCh37.p13 chr 4 NC_000004.11:g.166300460G>A
GRCh37.p13 chr 4 NC_000004.11:g.166300460G>C
GRCh37.p13 chr 4 NC_000004.11:g.166300460G>T
Gene: CPE, carboxypeptidase E (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CPE transcript NM_001873.4:c.87G>A E [GAG] > E [GAA] Coding Sequence Variant
carboxypeptidase E preproprotein NP_001864.1:p.Glu29= E (Glu) > E (Glu) Synonymous Variant
CPE transcript NM_001873.4:c.87G>C E [GAG] > D [GAC] Coding Sequence Variant
carboxypeptidase E preproprotein NP_001864.1:p.Glu29Asp E (Glu) > D (Asp) Missense Variant
CPE transcript NM_001873.4:c.87G>T E [GAG] > D [GAT] Coding Sequence Variant
carboxypeptidase E preproprotein NP_001864.1:p.Glu29Asp E (Glu) > D (Asp) Missense Variant

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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 14050 G=1.00000 A=0.00000, C=0.00000, T=0.00000
European Sub 9690 G=1.0000 A=0.0000, C=0.0000, T=0.0000
African Sub 2898 G=1.0000 A=0.0000, C=0.0000, T=0.0000
African Others Sub 114 G=1.000 A=0.000, C=0.000, T=0.000
African American Sub 2784 G=1.0000 A=0.0000, C=0.0000, T=0.0000
Asian Sub 112 G=1.000 A=0.000, C=0.000, T=0.000
East Asian Sub 86 G=1.00 A=0.00, C=0.00, T=0.00
Other Asian Sub 26 G=1.00 A=0.00, C=0.00, T=0.00
Latin American 1 Sub 146 G=1.000 A=0.000, C=0.000, T=0.000
Latin American 2 Sub 610 G=1.000 A=0.000, C=0.000, T=0.000
South Asian Sub 98 G=1.00 A=0.00, C=0.00, T=0.00
Other Sub 496 G=1.000 A=0.000, C=0.000, T=0.000


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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 147390 G=0.999993 C=0.000007
gnomAD - Exomes European Sub 66758 G=1.00000 C=0.00000
gnomAD - Exomes Asian Sub 35510 G=0.99997 C=0.00003
gnomAD - Exomes American Sub 25342 G=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 8114 G=1.0000 C=0.0000
gnomAD - Exomes African Sub 7450 G=1.0000 C=0.0000
gnomAD - Exomes Other Sub 4216 G=1.0000 C=0.0000
gnomAD - Genomes Global Study-wide 139982 G=0.999986 A=0.000014
gnomAD - Genomes European Sub 75754 G=1.00000 A=0.00000
gnomAD - Genomes African Sub 41994 G=0.99998 A=0.00002
gnomAD - Genomes American Sub 13632 G=0.99993 A=0.00007
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3128 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2150 G=1.0000 A=0.0000
ExAC Global Study-wide 12652 G=0.99992 C=0.00008
ExAC Asian Sub 7540 G=0.9999 C=0.0001
ExAC Europe Sub 4234 G=1.0000 C=0.0000
ExAC African Sub 526 G=1.000 C=0.000
ExAC American Sub 224 G=1.000 C=0.000
ExAC Other Sub 128 G=1.000 C=0.000

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= A C T
GRCh38.p13 chr 4 NC_000004.12:g.165379308= NC_000004.12:g.165379308G>A NC_000004.12:g.165379308G>C NC_000004.12:g.165379308G>T
GRCh37.p13 chr 4 NC_000004.11:g.166300460= NC_000004.11:g.166300460G>A NC_000004.11:g.166300460G>C NC_000004.11:g.166300460G>T
CPE transcript NM_001873.4:c.87= NM_001873.4:c.87G>A NM_001873.4:c.87G>C NM_001873.4:c.87G>T
CPE transcript NM_001873.3:c.87= NM_001873.3:c.87G>A NM_001873.3:c.87G>C NM_001873.3:c.87G>T
CPE transcript NM_001873.2:c.87= NM_001873.2:c.87G>A NM_001873.2:c.87G>C NM_001873.2:c.87G>T
carboxypeptidase E preproprotein NP_001864.1:p.Glu29= NP_001864.1:p.Glu29= NP_001864.1:p.Glu29Asp NP_001864.1:p.Glu29Asp

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#.

7 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1687685621 Apr 01, 2015 (144)
2 GNOMAD ss2734810290 Nov 08, 2017 (151)
3 TOPMED ss3449322342 Nov 08, 2017 (151)
4 GNOMAD ss4124774041 Apr 26, 2021 (155)
5 TOPMED ss4640699160 Apr 26, 2021 (155)
6 TOPMED ss4640699161 Apr 26, 2021 (155)
7 TOPMED ss4640699162 Apr 26, 2021 (155)
8 ExAC NC_000004.11 - 166300460 Oct 12, 2018 (152)
9 gnomAD - Genomes NC_000004.12 - 165379308 Apr 26, 2021 (155)
10 gnomAD - Exomes NC_000004.11 - 166300460 Jul 13, 2019 (153)
11 TopMed

Submission ignored due to conflicting rows:
Row 478076716 (NC_000004.12:165379307:G:A 2/264690)
Row 478076717 (NC_000004.12:165379307:G:C 1/264690)
Row 478076718 (NC_000004.12:165379307:G:T 2/264690)

- Apr 26, 2021 (155)
12 TopMed

Submission ignored due to conflicting rows:
Row 478076716 (NC_000004.12:165379307:G:A 2/264690)
Row 478076717 (NC_000004.12:165379307:G:C 1/264690)
Row 478076718 (NC_000004.12:165379307:G:T 2/264690)

- Apr 26, 2021 (155)
13 TopMed

Submission ignored due to conflicting rows:
Row 478076716 (NC_000004.12:165379307:G:A 2/264690)
Row 478076717 (NC_000004.12:165379307:G:C 1/264690)
Row 478076718 (NC_000004.12:165379307:G:T 2/264690)

- Apr 26, 2021 (155)
14 ALFA NC_000004.12 - 165379308 Apr 26, 2021 (155)

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
172269988, 298878575, 9660407817, ss3449322342, ss4124774041, ss4640699160 NC_000004.12:165379307:G:A NC_000004.12:165379307:G:A (self)
7666560, 3923234, ss1687685621, ss2734810290 NC_000004.11:166300459:G:C NC_000004.12:165379307:G:C (self)
9660407817, ss4640699161 NC_000004.12:165379307:G:C NC_000004.12:165379307:G:C
9660407817, ss4640699162 NC_000004.12:165379307:G:T NC_000004.12:165379307:G:T

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs778940259


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.post596+ae089ad