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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.

rs1470452230

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:135561895 (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 / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000007 (1/140100, GnomAD)
G=0.00000 (0/10680, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PAEP : Missense 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 A=1.00000 G=0.00000 1.0 0.0 0.0 N/A
European Sub 6962 A=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Sub 2294 A=1.0000 G=0.0000 1.0 0.0 0.0 N/A
African Others Sub 84 A=1.00 G=0.00 1.0 0.0 0.0 N/A
African American Sub 2210 A=1.0000 G=0.0000 1.0 0.0 0.0 N/A
Asian Sub 108 A=1.000 G=0.000 1.0 0.0 0.0 N/A
East Asian Sub 84 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Asian Sub 24 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 A=1.000 G=0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 A=1.000 G=0.000 1.0 0.0 0.0 N/A
South Asian Sub 94 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Sub 466 A=1.000 G=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
gnomAD - Genomes Global Study-wide 140100 A=0.999993 C=0.000007
gnomAD - Genomes European Sub 75858 A=0.99999 C=0.00001
gnomAD - Genomes African Sub 41994 A=1.00000 C=0.00000
gnomAD - Genomes American Sub 13656 A=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3318 A=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3126 A=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2148 A=1.0000 C=0.0000
Allele Frequency Aggregator Total Global 10680 A=1.00000 G=0.00000
Allele Frequency Aggregator European Sub 6962 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2294 A=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 G=0.000
Allele Frequency Aggregator Other Sub 466 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 108 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 94 A=1.00 G=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 9 NC_000009.12:g.135561895A>C
GRCh38.p14 chr 9 NC_000009.12:g.135561895A>G
GRCh37.p13 chr 9 NC_000009.11:g.138453741A>C
GRCh37.p13 chr 9 NC_000009.11:g.138453741A>G
Gene: PAEP, progestagen associated endometrial protein (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PAEP transcript variant 2 NM_002571.4:c.94A>C K [AAG] > Q [CAG] Coding Sequence Variant
glycodelin isoform 1 precursor NP_002562.2:p.Lys32Gln K (Lys) > Q (Gln) Missense Variant
PAEP transcript variant 2 NM_002571.4:c.94A>G K [AAG] > E [GAG] Coding Sequence Variant
glycodelin isoform 1 precursor NP_002562.2:p.Lys32Glu K (Lys) > E (Glu) Missense Variant
PAEP transcript variant 1 NM_001018049.3:c.94A>C K [AAG] > Q [CAG] Coding Sequence Variant
glycodelin isoform 1 precursor NP_001018059.1:p.Lys32Gln K (Lys) > Q (Gln) Missense Variant
PAEP transcript variant 1 NM_001018049.3:c.94A>G K [AAG] > E [GAG] Coding Sequence Variant
glycodelin isoform 1 precursor NP_001018059.1:p.Lys32Glu K (Lys) > E (Glu) Missense Variant
PAEP transcript variant 3 NM_001018048.2:c.94A>C K [AAG] > Q [CAG] Coding Sequence Variant
glycodelin isoform 2 precursor NP_001018058.1:p.Lys32Gln K (Lys) > Q (Gln) Missense Variant
PAEP transcript variant 3 NM_001018048.2:c.94A>G K [AAG] > E [GAG] Coding Sequence Variant
glycodelin isoform 2 precursor NP_001018058.1:p.Lys32Glu K (Lys) > E (Glu) Missense Variant
PAEP transcript variant X3 XM_011518747.2:c.94A>C K [AAG] > Q [CAG] Coding Sequence Variant
glycodelin isoform X1 XP_011517049.1:p.Lys32Gln K (Lys) > Q (Gln) Missense Variant
PAEP transcript variant X3 XM_011518747.2:c.94A>G K [AAG] > E [GAG] Coding Sequence Variant
glycodelin isoform X1 XP_011517049.1:p.Lys32Glu K (Lys) > E (Glu) Missense Variant
PAEP transcript variant X5 XM_011518749.2:c.94A>C K [AAG] > Q [CAG] Coding Sequence Variant
glycodelin isoform X3 XP_011517051.1:p.Lys32Gln K (Lys) > Q (Gln) Missense Variant
PAEP transcript variant X5 XM_011518749.2:c.94A>G K [AAG] > E [GAG] Coding Sequence Variant
glycodelin isoform X3 XP_011517051.1:p.Lys32Glu K (Lys) > E (Glu) Missense Variant
PAEP transcript variant X9 XM_017014783.2:c.94A>C K [AAG] > Q [CAG] Coding Sequence Variant
glycodelin isoform X7 XP_016870272.1:p.Lys32Gln K (Lys) > Q (Gln) Missense Variant
PAEP transcript variant X9 XM_017014783.2:c.94A>G K [AAG] > E [GAG] Coding Sequence Variant
glycodelin isoform X7 XP_016870272.1:p.Lys32Glu K (Lys) > E (Glu) Missense Variant
PAEP transcript variant X1 XM_011518745.3:c.94A>C K [AAG] > Q [CAG] Coding Sequence Variant
glycodelin isoform X1 XP_011517047.1:p.Lys32Gln K (Lys) > Q (Gln) Missense Variant
PAEP transcript variant X1 XM_011518745.3:c.94A>G K [AAG] > E [GAG] Coding Sequence Variant
glycodelin isoform X1 XP_011517047.1:p.Lys32Glu K (Lys) > E (Glu) Missense Variant
PAEP transcript variant X2 XM_011518746.3:c.94A>C K [AAG] > Q [CAG] Coding Sequence Variant
glycodelin isoform X1 XP_011517048.1:p.Lys32Gln K (Lys) > Q (Gln) Missense Variant
PAEP transcript variant X2 XM_011518746.3:c.94A>G K [AAG] > E [GAG] Coding Sequence Variant
glycodelin isoform X1 XP_011517048.1:p.Lys32Glu K (Lys) > E (Glu) Missense Variant
PAEP transcript variant X4 XM_011518748.2:c.94A>C K [AAG] > Q [CAG] Coding Sequence Variant
glycodelin isoform X2 XP_011517050.1:p.Lys32Gln K (Lys) > Q (Gln) Missense Variant
PAEP transcript variant X4 XM_011518748.2:c.94A>G K [AAG] > E [GAG] Coding Sequence Variant
glycodelin isoform X2 XP_011517050.1:p.Lys32Glu K (Lys) > E (Glu) Missense Variant
PAEP transcript variant X6 XM_011518751.2:c.94A>C K [AAG] > Q [CAG] Coding Sequence Variant
glycodelin isoform X4 XP_011517053.1:p.Lys32Gln K (Lys) > Q (Gln) Missense Variant
PAEP transcript variant X6 XM_011518751.2:c.94A>G K [AAG] > E [GAG] Coding Sequence Variant
glycodelin isoform X4 XP_011517053.1:p.Lys32Glu K (Lys) > E (Glu) Missense Variant
PAEP transcript variant X7 XM_011518752.3:c.94A>C K [AAG] > Q [CAG] Coding Sequence Variant
glycodelin isoform X5 XP_011517054.1:p.Lys32Gln K (Lys) > Q (Gln) Missense Variant
PAEP transcript variant X7 XM_011518752.3:c.94A>G K [AAG] > E [GAG] Coding Sequence Variant
glycodelin isoform X5 XP_011517054.1:p.Lys32Glu K (Lys) > E (Glu) Missense Variant
PAEP transcript variant X8 XM_017014782.3:c.94A>C K [AAG] > Q [CAG] Coding Sequence Variant
glycodelin isoform X6 XP_016870271.1:p.Lys32Gln K (Lys) > Q (Gln) Missense Variant
PAEP transcript variant X8 XM_017014782.3:c.94A>G K [AAG] > E [GAG] Coding Sequence Variant
glycodelin isoform X6 XP_016870271.1:p.Lys32Glu K (Lys) > E (Glu) 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 G
GRCh38.p14 chr 9 NC_000009.12:g.135561895= NC_000009.12:g.135561895A>C NC_000009.12:g.135561895A>G
GRCh37.p13 chr 9 NC_000009.11:g.138453741= NC_000009.11:g.138453741A>C NC_000009.11:g.138453741A>G
PAEP transcript variant 2 NM_002571.4:c.94= NM_002571.4:c.94A>C NM_002571.4:c.94A>G
PAEP transcript variant 2 NM_002571.3:c.94= NM_002571.3:c.94A>C NM_002571.3:c.94A>G
PAEP transcript variant 2 NM_002571.2:c.94= NM_002571.2:c.94A>C NM_002571.2:c.94A>G
PAEP transcript variant X2 XM_011518746.3:c.94= XM_011518746.3:c.94A>C XM_011518746.3:c.94A>G
PAEP transcript variant X2 XM_011518746.2:c.94= XM_011518746.2:c.94A>C XM_011518746.2:c.94A>G
PAEP transcript variant X2 XM_011518746.1:c.94= XM_011518746.1:c.94A>C XM_011518746.1:c.94A>G
PAEP transcript variant X1 XM_011518745.3:c.94= XM_011518745.3:c.94A>C XM_011518745.3:c.94A>G
PAEP transcript variant X1 XM_011518745.2:c.94= XM_011518745.2:c.94A>C XM_011518745.2:c.94A>G
PAEP transcript variant X1 XM_011518745.1:c.94= XM_011518745.1:c.94A>C XM_011518745.1:c.94A>G
PAEP transcript variant 1 NM_001018049.3:c.94= NM_001018049.3:c.94A>C NM_001018049.3:c.94A>G
PAEP transcript variant 1 NM_001018049.2:c.94= NM_001018049.2:c.94A>C NM_001018049.2:c.94A>G
PAEP transcript variant 1 NM_001018049.1:c.94= NM_001018049.1:c.94A>C NM_001018049.1:c.94A>G
PAEP transcript variant X7 XM_011518752.3:c.94= XM_011518752.3:c.94A>C XM_011518752.3:c.94A>G
PAEP transcript variant X7 XM_011518752.2:c.94= XM_011518752.2:c.94A>C XM_011518752.2:c.94A>G
PAEP transcript variant X9 XM_011518752.1:c.94= XM_011518752.1:c.94A>C XM_011518752.1:c.94A>G
PAEP transcript variant X8 XM_017014782.3:c.94= XM_017014782.3:c.94A>C XM_017014782.3:c.94A>G
PAEP transcript variant X8 XM_017014782.2:c.94= XM_017014782.2:c.94A>C XM_017014782.2:c.94A>G
PAEP transcript variant X8 XM_017014782.1:c.94= XM_017014782.1:c.94A>C XM_017014782.1:c.94A>G
PAEP transcript variant X4 XM_011518748.2:c.94= XM_011518748.2:c.94A>C XM_011518748.2:c.94A>G
PAEP transcript variant X4 XM_011518748.1:c.94= XM_011518748.1:c.94A>C XM_011518748.1:c.94A>G
PAEP transcript variant X6 XM_011518751.2:c.94= XM_011518751.2:c.94A>C XM_011518751.2:c.94A>G
PAEP transcript variant X6 XM_011518751.1:c.94= XM_011518751.1:c.94A>C XM_011518751.1:c.94A>G
PAEP transcript variant 3 NM_001018048.2:c.94= NM_001018048.2:c.94A>C NM_001018048.2:c.94A>G
PAEP transcript variant 3 NM_001018048.1:c.94= NM_001018048.1:c.94A>C NM_001018048.1:c.94A>G
PAEP transcript variant X3 XM_011518747.2:c.94= XM_011518747.2:c.94A>C XM_011518747.2:c.94A>G
PAEP transcript variant X3 XM_011518747.1:c.94= XM_011518747.1:c.94A>C XM_011518747.1:c.94A>G
PAEP transcript variant X5 XM_011518749.2:c.94= XM_011518749.2:c.94A>C XM_011518749.2:c.94A>G
PAEP transcript variant X5 XM_011518749.1:c.94= XM_011518749.1:c.94A>C XM_011518749.1:c.94A>G
PAEP transcript variant X9 XM_017014783.2:c.94= XM_017014783.2:c.94A>C XM_017014783.2:c.94A>G
PAEP transcript variant X9 XM_017014783.1:c.94= XM_017014783.1:c.94A>C XM_017014783.1:c.94A>G
glycodelin isoform 1 precursor NP_002562.2:p.Lys32= NP_002562.2:p.Lys32Gln NP_002562.2:p.Lys32Glu
glycodelin isoform X1 XP_011517048.1:p.Lys32= XP_011517048.1:p.Lys32Gln XP_011517048.1:p.Lys32Glu
glycodelin isoform X1 XP_011517047.1:p.Lys32= XP_011517047.1:p.Lys32Gln XP_011517047.1:p.Lys32Glu
glycodelin isoform 1 precursor NP_001018059.1:p.Lys32= NP_001018059.1:p.Lys32Gln NP_001018059.1:p.Lys32Glu
glycodelin isoform X5 XP_011517054.1:p.Lys32= XP_011517054.1:p.Lys32Gln XP_011517054.1:p.Lys32Glu
glycodelin isoform X6 XP_016870271.1:p.Lys32= XP_016870271.1:p.Lys32Gln XP_016870271.1:p.Lys32Glu
glycodelin isoform X2 XP_011517050.1:p.Lys32= XP_011517050.1:p.Lys32Gln XP_011517050.1:p.Lys32Glu
glycodelin isoform X4 XP_011517053.1:p.Lys32= XP_011517053.1:p.Lys32Gln XP_011517053.1:p.Lys32Glu
glycodelin isoform 2 precursor NP_001018058.1:p.Lys32= NP_001018058.1:p.Lys32Gln NP_001018058.1:p.Lys32Glu
glycodelin isoform X1 XP_011517049.1:p.Lys32= XP_011517049.1:p.Lys32Gln XP_011517049.1:p.Lys32Glu
glycodelin isoform X3 XP_011517051.1:p.Lys32= XP_011517051.1:p.Lys32Gln XP_011517051.1:p.Lys32Glu
glycodelin isoform X7 XP_016870272.1:p.Lys32= XP_016870272.1:p.Lys32Gln XP_016870272.1:p.Lys32Glu
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, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 GNOMAD ss2748307101 Nov 08, 2017 (151)
2 GNOMAD ss2884240097 Nov 08, 2017 (151)
3 gnomAD - Genomes NC_000009.12 - 135561895 Apr 26, 2021 (155)
4 ALFA NC_000009.12 - 135561895 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
ss2748307101, ss2884240097 NC_000009.11:138453740:A:C NC_000009.12:135561894:A:C (self)
340250769 NC_000009.12:135561894:A:C NC_000009.12:135561894:A:C (self)
13589025861 NC_000009.12:135561894:A:G NC_000009.12:135561894:A:G (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 rs1470452230

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