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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.

rs1057519516

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:9734707 (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
delT
Variation Type
Deletion
Frequency
None
Clinical Significance
Reported in ClinVar
Gene : Consequence
BRPF1 : Frameshift Variant
Publications
1 citation
Genomic View
See rs on genome
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").

None
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.9734707del
GRCh37.p13 chr 3 NC_000003.11:g.9776391del
BRPF1 RefSeqGene NG_052955.1:g.7979del
Gene: BRPF1, bromodomain and PHD finger containing 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
BRPF1 transcript variant 1 NM_001003694.2:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform 1 NP_001003694.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant 4 NM_001319050.2:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform 4 NP_001305979.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant 3 NM_001319049.2:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform 3 NP_001305978.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant 2 NM_004634.3:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform 2 NP_004625.2:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant 5 NR_160918.1:n.981del N/A Non Coding Transcript Variant
BRPF1 transcript variant X1 XM_011534101.2:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform X1 XP_011532403.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant X2 XM_047448875.1:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform X1 XP_047304831.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant X3 XM_005265449.2:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform X2 XP_005265506.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant X4 XM_047448876.1:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform X3 XP_047304832.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant X5 XM_005265450.2:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform X4 XP_005265507.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant X5 XM_047448877.1:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform X4 XP_047304833.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant X6 XM_047448878.1:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform X5 XP_047304834.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant X7 XM_047448879.1:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform X6 XP_047304835.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant X9 XM_047448880.1:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform X7 XP_047304836.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant X9 XM_047448881.1:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform X7 XP_047304837.1:p.Asp190fs P (Pro) > P (Pro) Frameshift Variant
BRPF1 transcript variant X10 XM_047448882.1:c.567del P [CCT] > P [CC] Coding Sequence Variant
peregrin isoform X7 XP_047304838.1:p.Asp190fs P (Pro) > P (Pro) Frameshift 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.

Allele: delT (allele ID: 362302 )
ClinVar Accession Disease Names Clinical Significance
RCV000417029.3 Intellectual developmental disorder with dysmorphic facies and ptosis Pathogenic
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 T= delT
GRCh38.p14 chr 3 NC_000003.12:g.9734707= NC_000003.12:g.9734707del
GRCh37.p13 chr 3 NC_000003.11:g.9776391= NC_000003.11:g.9776391del
BRPF1 RefSeqGene NG_052955.1:g.7979= NG_052955.1:g.7979del
BRPF1 transcript variant 2 NM_004634.3:c.567= NM_004634.3:c.567del
BRPF1 transcript variant 2 NM_004634.2:c.567= NM_004634.2:c.567del
BRPF1 transcript variant 1 NM_001003694.2:c.567= NM_001003694.2:c.567del
BRPF1 transcript variant 1 NM_001003694.1:c.567= NM_001003694.1:c.567del
BRPF1 transcript variant 4 NM_001319050.2:c.567= NM_001319050.2:c.567del
BRPF1 transcript variant 4 NM_001319050.1:c.567= NM_001319050.1:c.567del
BRPF1 transcript variant 3 NM_001319049.2:c.567= NM_001319049.2:c.567del
BRPF1 transcript variant 3 NM_001319049.1:c.567= NM_001319049.1:c.567del
BRPF1 transcript variant 5 NR_160918.1:n.981= NR_160918.1:n.981del
BRPF1 transcript variant 6 NM_001410704.1:c.567= NM_001410704.1:c.567del
BRPF1 transcript variant X1 XM_011534101.2:c.567= XM_011534101.2:c.567del
BRPF1 transcript variant X4 XM_011534101.1:c.567= XM_011534101.1:c.567del
BRPF1 transcript variant X3 XM_005265449.2:c.567= XM_005265449.2:c.567del
BRPF1 transcript variant X5 XM_005265449.1:c.567= XM_005265449.1:c.567del
BRPF1 transcript variant X5 XM_005265450.2:c.567= XM_005265450.2:c.567del
BRPF1 transcript variant X4 XM_047448876.1:c.567= XM_047448876.1:c.567del
BRPF1 transcript variant X9 XM_047448880.1:c.567= XM_047448880.1:c.567del
BRPF1 transcript variant X10 XM_047448882.1:c.567= XM_047448882.1:c.567del
BRPF1 transcript variant X2 XM_047448875.1:c.567= XM_047448875.1:c.567del
BRPF1 transcript variant X5 XM_047448877.1:c.567= XM_047448877.1:c.567del
BRPF1 transcript variant X6 XM_047448878.1:c.567= XM_047448878.1:c.567del
BRPF1 transcript variant X7 XM_047448879.1:c.567= XM_047448879.1:c.567del
BRPF1 transcript variant X9 XM_047448881.1:c.567= XM_047448881.1:c.567del
peregrin isoform 2 NP_004625.2:p.Pro189= NP_004625.2:p.Asp190fs
peregrin isoform 1 NP_001003694.1:p.Pro189= NP_001003694.1:p.Asp190fs
peregrin isoform 4 NP_001305979.1:p.Pro189= NP_001305979.1:p.Asp190fs
peregrin isoform 3 NP_001305978.1:p.Pro189= NP_001305978.1:p.Asp190fs
peregrin isoform X1 XP_011532403.1:p.Pro189= XP_011532403.1:p.Asp190fs
peregrin isoform X2 XP_005265506.1:p.Pro189= XP_005265506.1:p.Asp190fs
peregrin isoform X4 XP_005265507.1:p.Pro189= XP_005265507.1:p.Asp190fs
peregrin isoform X3 XP_047304832.1:p.Pro189= XP_047304832.1:p.Asp190fs
peregrin isoform X7 XP_047304836.1:p.Pro189= XP_047304836.1:p.Asp190fs
peregrin isoform X7 XP_047304838.1:p.Pro189= XP_047304838.1:p.Asp190fs
peregrin isoform X1 XP_047304831.1:p.Pro189= XP_047304831.1:p.Asp190fs
peregrin isoform X4 XP_047304833.1:p.Pro189= XP_047304833.1:p.Asp190fs
peregrin isoform X5 XP_047304834.1:p.Pro189= XP_047304834.1:p.Asp190fs
peregrin isoform X6 XP_047304835.1:p.Pro189= XP_047304835.1:p.Asp190fs
peregrin isoform X7 XP_047304837.1:p.Pro189= XP_047304837.1:p.Asp190fs
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#.

1 SubSNP, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 CLINVAR ss2137497366 Feb 23, 2017 (149)
2 ClinVar RCV000417029.3 Oct 13, 2022 (156)
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
RCV000417029.3, ss2137497366 NC_000003.12:9734706:T: NC_000003.12:9734706:T: (self)
Help

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

1 citation for rs1057519516
PMID Title Author Year Journal
27939639 Mutations in Histone Acetylase Modifier BRPF1 Cause an Autosomal-Dominant Form of Intellectual Disability with Associated Ptosis. Mattioli F et al. 2017 American journal of human genetics
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