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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.

rs545050848

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:189866776 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000008 (2/264690, TOPMED)
A=0.000012 (3/251332, GnomAD_exome)
A=0.000007 (1/140154, GnomAD) (+ 4 more)
A=0.000025 (3/121312, ExAC)
A=0.00000 (0/14050, ALFA)
A=0.0003 (2/6404, 1000G_30x)
A=0.0002 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
TP63 : Synonymous 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: 20230706150541
Population Group Sample Size Ref Allele Alt Allele
Total Global 14050 G=1.00000 A=0.00000
European Sub 9690 G=1.0000 A=0.0000
African Sub 2898 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 2784 G=1.0000 A=0.0000
Asian Sub 112 G=1.000 A=0.000
East Asian Sub 86 G=1.00 A=0.00
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 496 G=1.000 A=0.000


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 G=0.999992 A=0.000008
gnomAD - Exomes Global Study-wide 251332 G=0.999988 A=0.000012
gnomAD - Exomes European Sub 135306 G=0.999993 A=0.000007
gnomAD - Exomes Asian Sub 48982 G=0.99996 A=0.00004
gnomAD - Exomes American Sub 34582 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 16256 G=1.00000 A=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10074 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6132 G=1.0000 A=0.0000
gnomAD - Genomes Global Study-wide 140154 G=0.999993 A=0.000007
gnomAD - Genomes European Sub 75896 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 42006 G=1.00000 A=0.00000
gnomAD - Genomes American Sub 13642 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 G=1.0000 A=0.0000
ExAC Global Study-wide 121312 G=0.999975 A=0.000025
ExAC Europe Sub 73306 G=0.99999 A=0.00001
ExAC Asian Sub 25126 G=0.99992 A=0.00008
ExAC American Sub 11566 G=1.00000 A=0.00000
ExAC African Sub 10406 G=1.00000 A=0.00000
ExAC Other Sub 908 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 14050 G=1.00000 A=0.00000
Allele Frequency Aggregator European Sub 9690 G=1.0000 A=0.0000
Allele Frequency Aggregator African Sub 2898 G=1.0000 A=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Other Sub 496 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9997 A=0.0003
1000Genomes_30x African Sub 1786 G=1.0000 A=0.0000
1000Genomes_30x Europe Sub 1266 G=1.0000 A=0.0000
1000Genomes_30x South Asian Sub 1202 G=0.9983 A=0.0017
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.9998 A=0.0002
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=0.999 A=0.001
1000Genomes American Sub 694 G=1.000 A=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 3 NC_000003.12:g.189866776G>A
GRCh37.p13 chr 3 NC_000003.11:g.189584565G>A
TP63 RefSeqGene (LRG_428) NG_007550.3:g.275031G>A
Gene: TP63, tumor protein p63 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
TP63 transcript variant 1 NM_003722.5:c.861G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 1 NP_003713.3:p.Leu287= L (Leu) > L (Leu) Synonymous Variant
TP63 transcript variant 4 NM_001114980.2:c.579G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 4 NP_001108452.1:p.Leu193= L (Leu) > L (Leu) Synonymous Variant
TP63 transcript variant 3 NM_001114979.2:c.861G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 3 NP_001108451.1:p.Leu287= L (Leu) > L (Leu) Synonymous Variant
TP63 transcript variant 6 NM_001114982.2:c.579G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 6 NP_001108454.1:p.Leu193= L (Leu) > L (Leu) Synonymous Variant
TP63 transcript variant 5 NM_001114981.2:c.579G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 5 NP_001108453.1:p.Leu193= L (Leu) > L (Leu) Synonymous Variant
TP63 transcript variant 8 NM_001329145.2:c.579G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 8 NP_001316074.1:p.Leu193= L (Leu) > L (Leu) Synonymous Variant
TP63 transcript variant 7 NM_001329144.2:c.861G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 7 NP_001316073.1:p.Leu287= L (Leu) > L (Leu) Synonymous Variant
TP63 transcript variant 12 NM_001329150.2:c.324G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 12 NP_001316079.1:p.Leu108= L (Leu) > L (Leu) Synonymous Variant
TP63 transcript variant 2 NM_001114978.2:c.861G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 2 NP_001108450.1:p.Leu287= L (Leu) > L (Leu) Synonymous Variant
TP63 transcript variant 11 NM_001329149.2:c.579G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 11 NP_001316078.1:p.Leu193= L (Leu) > L (Leu) Synonymous Variant
TP63 transcript variant 9 NM_001329146.2:c.324G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 9 NP_001316075.1:p.Leu108= L (Leu) > L (Leu) Synonymous Variant
TP63 transcript variant 10 NM_001329148.2:c.861G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 10 NP_001316077.1:p.Leu287= L (Leu) > L (Leu) Synonymous Variant
TP63 transcript variant 13 NM_001329964.2:c.855G>A L [CTG] > L [CTA] Coding Sequence Variant
tumor protein 63 isoform 13 NP_001316893.1:p.Leu285= L (Leu) > L (Leu) Synonymous 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 G= A
GRCh38.p14 chr 3 NC_000003.12:g.189866776= NC_000003.12:g.189866776G>A
GRCh37.p13 chr 3 NC_000003.11:g.189584565= NC_000003.11:g.189584565G>A
TP63 RefSeqGene (LRG_428) NG_007550.3:g.275031= NG_007550.3:g.275031G>A
TP63 transcript variant 1 NM_003722.5:c.861= NM_003722.5:c.861G>A
TP63 transcript variant 1 NM_003722.4:c.861= NM_003722.4:c.861G>A
TP63 transcript variant 13 NM_001329964.2:c.855= NM_001329964.2:c.855G>A
TP63 transcript variant 13 NM_001329964.1:c.855= NM_001329964.1:c.855G>A
TP63 transcript variant 10 NM_001329148.2:c.861= NM_001329148.2:c.861G>A
TP63 transcript variant 10 NM_001329148.1:c.861= NM_001329148.1:c.861G>A
TP63 transcript variant 2 NM_001114978.2:c.861= NM_001114978.2:c.861G>A
TP63 transcript variant 2 NM_001114978.1:c.861= NM_001114978.1:c.861G>A
TP63 transcript variant 7 NM_001329144.2:c.861= NM_001329144.2:c.861G>A
TP63 transcript variant 7 NM_001329144.1:c.861= NM_001329144.1:c.861G>A
TP63 transcript variant 4 NM_001114980.2:c.579= NM_001114980.2:c.579G>A
TP63 transcript variant 4 NM_001114980.1:c.579= NM_001114980.1:c.579G>A
TP63 transcript variant 5 NM_001114981.2:c.579= NM_001114981.2:c.579G>A
TP63 transcript variant 5 NM_001114981.1:c.579= NM_001114981.1:c.579G>A
TP63 transcript variant 8 NM_001329145.2:c.579= NM_001329145.2:c.579G>A
TP63 transcript variant 8 NM_001329145.1:c.579= NM_001329145.1:c.579G>A
TP63 transcript variant 11 NM_001329149.2:c.579= NM_001329149.2:c.579G>A
TP63 transcript variant 11 NM_001329149.1:c.579= NM_001329149.1:c.579G>A
TP63 transcript variant 9 NM_001329146.2:c.324= NM_001329146.2:c.324G>A
TP63 transcript variant 9 NM_001329146.1:c.324= NM_001329146.1:c.324G>A
TP63 transcript variant 12 NM_001329150.2:c.324= NM_001329150.2:c.324G>A
TP63 transcript variant 12 NM_001329150.1:c.324= NM_001329150.1:c.324G>A
TP63 transcript variant 3 NM_001114979.2:c.861= NM_001114979.2:c.861G>A
TP63 transcript variant 3 NM_001114979.1:c.861= NM_001114979.1:c.861G>A
TP63 transcript variant 6 NM_001114982.2:c.579= NM_001114982.2:c.579G>A
TP63 transcript variant 6 NM_001114982.1:c.579= NM_001114982.1:c.579G>A
tumor protein 63 isoform 1 NP_003713.3:p.Leu287= NP_003713.3:p.Leu287=
tumor protein 63 isoform 13 NP_001316893.1:p.Leu285= NP_001316893.1:p.Leu285=
tumor protein 63 isoform 10 NP_001316077.1:p.Leu287= NP_001316077.1:p.Leu287=
tumor protein 63 isoform 2 NP_001108450.1:p.Leu287= NP_001108450.1:p.Leu287=
tumor protein 63 isoform 7 NP_001316073.1:p.Leu287= NP_001316073.1:p.Leu287=
tumor protein 63 isoform 4 NP_001108452.1:p.Leu193= NP_001108452.1:p.Leu193=
tumor protein 63 isoform 5 NP_001108453.1:p.Leu193= NP_001108453.1:p.Leu193=
tumor protein 63 isoform 8 NP_001316074.1:p.Leu193= NP_001316074.1:p.Leu193=
tumor protein 63 isoform 11 NP_001316078.1:p.Leu193= NP_001316078.1:p.Leu193=
tumor protein 63 isoform 9 NP_001316075.1:p.Leu108= NP_001316075.1:p.Leu108=
tumor protein 63 isoform 12 NP_001316079.1:p.Leu108= NP_001316079.1:p.Leu108=
tumor protein 63 isoform 3 NP_001108451.1:p.Leu287= NP_001108451.1:p.Leu287=
tumor protein 63 isoform 6 NP_001108454.1:p.Leu193= NP_001108454.1:p.Leu193=
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#.

9 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss1307778483 Aug 21, 2014 (142)
2 EVA_EXAC ss1687338058 Apr 01, 2015 (144)
3 GNOMAD ss2734269486 Nov 08, 2017 (151)
4 GNOMAD ss4087926826 Apr 26, 2021 (155)
5 TOPMED ss4597747299 Apr 26, 2021 (155)
6 1000G_HIGH_COVERAGE ss5257449066 Oct 13, 2022 (156)
7 EVA ss5345868730 Oct 13, 2022 (156)
8 1000G_HIGH_COVERAGE ss5537630955 Oct 13, 2022 (156)
9 EVA ss5872631665 Oct 13, 2022 (156)
10 1000Genomes NC_000003.11 - 189584565 Oct 12, 2018 (152)
11 1000Genomes_30x NC_000003.12 - 189866776 Oct 13, 2022 (156)
12 ExAC NC_000003.11 - 189584565 Oct 12, 2018 (152)
13 gnomAD - Genomes NC_000003.12 - 189866776 Apr 26, 2021 (155)
14 gnomAD - Exomes NC_000003.11 - 189584565 Jul 13, 2019 (153)
15 TopMed NC_000003.12 - 189866776 Apr 26, 2021 (155)
16 ALFA NC_000003.12 - 189866776 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
19104490, 7288581, 3364768, ss1307778483, ss1687338058, ss2734269486, ss5345868730 NC_000003.11:189584564:G:A NC_000003.12:189866775:G:A (self)
25156890, 135694246, 435124854, 3329236162, ss4087926826, ss4597747299, ss5257449066, ss5537630955, ss5872631665 NC_000003.12:189866775:G:A NC_000003.12:189866775:G:A (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 rs545050848

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.post761+d5e8e07