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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.

rs1491559772

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:25348667-25348668 (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
delAA
Variation Type
Deletion
Frequency
delAA=0.000030 (8/264690, TOPMED)
delAA=0.000057 (8/140064, GnomAD)
delAA=0.00000 (0/14050, ALFA)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SNHG14 : Intron Variant
UBE3A : Intron 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 14050 AA=1.00000 =0.00000 1.0 0.0 0.0 N/A
European Sub 9690 AA=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Sub 2898 AA=1.0000 =0.0000 1.0 0.0 0.0 N/A
African Others Sub 114 AA=1.000 =0.000 1.0 0.0 0.0 N/A
African American Sub 2784 AA=1.0000 =0.0000 1.0 0.0 0.0 N/A
Asian Sub 112 AA=1.000 =0.000 1.0 0.0 0.0 N/A
East Asian Sub 86 AA=1.00 =0.00 1.0 0.0 0.0 N/A
Other Asian Sub 26 AA=1.00 =0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 146 AA=1.000 =0.000 1.0 0.0 0.0 N/A
Latin American 2 Sub 610 AA=1.000 =0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 AA=1.00 =0.00 1.0 0.0 0.0 N/A
Other Sub 496 AA=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 AA=0.999970 delAA=0.000030
gnomAD - Genomes Global Study-wide 140064 AA=0.999943 delAA=0.000057
gnomAD - Genomes European Sub 75850 AA=0.99991 delAA=0.00009
gnomAD - Genomes African Sub 41972 AA=1.00000 delAA=0.00000
gnomAD - Genomes American Sub 13644 AA=1.00000 delAA=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 AA=1.0000 delAA=0.0000
gnomAD - Genomes East Asian Sub 3126 AA=1.0000 delAA=0.0000
gnomAD - Genomes Other Sub 2152 AA=0.9995 delAA=0.0005
Allele Frequency Aggregator Total Global 14050 AA=1.00000 delAA=0.00000
Allele Frequency Aggregator European Sub 9690 AA=1.0000 delAA=0.0000
Allele Frequency Aggregator African Sub 2898 AA=1.0000 delAA=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 AA=1.000 delAA=0.000
Allele Frequency Aggregator Other Sub 496 AA=1.000 delAA=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 AA=1.000 delAA=0.000
Allele Frequency Aggregator Asian Sub 112 AA=1.000 delAA=0.000
Allele Frequency Aggregator South Asian Sub 98 AA=1.00 delAA=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 15 NC_000015.10:g.25348667_25348668del
GRCh37.p13 chr 15 NC_000015.9:g.25593814_25593815del
PWSAS genomic region NG_002690.1:g.567758_567759del
UBE3A RefSeqGene (LRG_15) NG_009268.1:g.95314_95315del
Gene: UBE3A, ubiquitin protein ligase E3A (minus strand)
Molecule type Change Amino acid[Codon] SO Term
UBE3A transcript variant 2 NM_000462.5:c.2363+5685_2…

NM_000462.5:c.2363+5685_2363+5686del

N/A Intron Variant
UBE3A transcript variant 4 NM_001354505.1:c.2354+568…

NM_001354505.1:c.2354+5685_2354+5686del

N/A Intron Variant
UBE3A transcript variant 5 NM_001354506.2:c.2294+568…

NM_001354506.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 6 NM_001354507.2:c.2294+568…

NM_001354507.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 7 NM_001354508.2:c.2294+568…

NM_001354508.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 8 NM_001354509.2:c.2294+568…

NM_001354509.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 10 NM_001354511.2:c.2294+568…

NM_001354511.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 11 NM_001354512.2:c.2294+568…

NM_001354512.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 12 NM_001354513.2:c.2294+568…

NM_001354513.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 9 NM_001354523.2:c.2294+568…

NM_001354523.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 13 NM_001354526.1:c.2294+568…

NM_001354526.1:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 14 NM_001354538.2:c.2354+568…

NM_001354538.2:c.2354+5685_2354+5686del

N/A Intron Variant
UBE3A transcript variant 15 NM_001354539.2:c.2294+568…

NM_001354539.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 16 NM_001354540.2:c.2294+568…

NM_001354540.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 17 NM_001354541.2:c.2294+568…

NM_001354541.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 18 NM_001354542.2:c.2294+568…

NM_001354542.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 19 NM_001354543.2:c.2294+568…

NM_001354543.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 20 NM_001354544.2:c.2294+568…

NM_001354544.2:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 21 NM_001354545.2:c.2198+568…

NM_001354545.2:c.2198+5685_2198+5686del

N/A Intron Variant
UBE3A transcript variant 22 NM_001354546.2:c.2177+568…

NM_001354546.2:c.2177+5685_2177+5686del

N/A Intron Variant
UBE3A transcript variant 23 NM_001354547.2:c.2138+568…

NM_001354547.2:c.2138+5685_2138+5686del

N/A Intron Variant
UBE3A transcript variant 24 NM_001354548.2:c.2138+568…

NM_001354548.2:c.2138+5685_2138+5686del

N/A Intron Variant
UBE3A transcript variant 25 NM_001354549.2:c.2129+568…

NM_001354549.2:c.2129+5685_2129+5686del

N/A Intron Variant
UBE3A transcript variant 26 NM_001354550.2:c.1103+568…

NM_001354550.2:c.1103+5685_1103+5686del

N/A Intron Variant
UBE3A transcript variant 27 NM_001354551.2:c.1043+568…

NM_001354551.2:c.1043+5685_1043+5686del

N/A Intron Variant
UBE3A transcript variant 29 NM_001374461.1:c.2294+568…

NM_001374461.1:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 1 NM_130838.4:c.2294+5685_2…

NM_130838.4:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant 3 NM_130839.5:c.2354+5685_2…

NM_130839.5:c.2354+5685_2354+5686del

N/A Intron Variant
UBE3A transcript variant 28 NR_148916.2:n. N/A Intron Variant
UBE3A transcript variant X3 XM_011521995.4:c.2363+568…

XM_011521995.4:c.2363+5685_2363+5686del

N/A Intron Variant
UBE3A transcript variant X7 XM_017022547.3:c.2354+568…

XM_017022547.3:c.2354+5685_2354+5686del

N/A Intron Variant
UBE3A transcript variant X10 XM_017022548.3:c.2354+568…

XM_017022548.3:c.2354+5685_2354+5686del

N/A Intron Variant
UBE3A transcript variant X14 XM_017022550.3:c.2354+568…

XM_017022550.3:c.2354+5685_2354+5686del

N/A Intron Variant
UBE3A transcript variant X2 XM_024450043.2:c.2363+568…

XM_024450043.2:c.2363+5685_2363+5686del

N/A Intron Variant
UBE3A transcript variant X1 XM_047433007.1:c.2363+568…

XM_047433007.1:c.2363+5685_2363+5686del

N/A Intron Variant
UBE3A transcript variant X4 XM_047433008.1:c.2363+568…

XM_047433008.1:c.2363+5685_2363+5686del

N/A Intron Variant
UBE3A transcript variant X5 XM_047433009.1:c.2363+568…

XM_047433009.1:c.2363+5685_2363+5686del

N/A Intron Variant
UBE3A transcript variant X6 XM_047433010.1:c.2363+568…

XM_047433010.1:c.2363+5685_2363+5686del

N/A Intron Variant
UBE3A transcript variant X8 XM_047433011.1:c.2354+568…

XM_047433011.1:c.2354+5685_2354+5686del

N/A Intron Variant
UBE3A transcript variant X9 XM_047433012.1:c.2354+568…

XM_047433012.1:c.2354+5685_2354+5686del

N/A Intron Variant
UBE3A transcript variant X11 XM_047433013.1:c.2354+568…

XM_047433013.1:c.2354+5685_2354+5686del

N/A Intron Variant
UBE3A transcript variant X12 XM_047433014.1:c.2354+568…

XM_047433014.1:c.2354+5685_2354+5686del

N/A Intron Variant
UBE3A transcript variant X13 XM_047433015.1:c.2354+568…

XM_047433015.1:c.2354+5685_2354+5686del

N/A Intron Variant
UBE3A transcript variant X15 XM_047433016.1:c.2294+568…

XM_047433016.1:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant X16 XM_047433017.1:c.2294+568…

XM_047433017.1:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant X17 XM_047433018.1:c.2294+568…

XM_047433018.1:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant X18 XM_047433019.1:c.2294+568…

XM_047433019.1:c.2294+5685_2294+5686del

N/A Intron Variant
UBE3A transcript variant X19 XM_047433020.1:c.2207+568…

XM_047433020.1:c.2207+5685_2207+5686del

N/A Intron Variant
UBE3A transcript variant X20 XM_047433021.1:c.2198+568…

XM_047433021.1:c.2198+5685_2198+5686del

N/A Intron Variant
Gene: SNHG14, small nucleolar RNA host gene 14 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SNHG14 transcript NR_146177.1: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 AA= delAA
GRCh38.p14 chr 15 NC_000015.10:g.25348667_25348668= NC_000015.10:g.25348667_25348668del
GRCh37.p13 chr 15 NC_000015.9:g.25593814_25593815= NC_000015.9:g.25593814_25593815del
PWSAS genomic region NG_002690.1:g.567758_567759= NG_002690.1:g.567758_567759del
UBE3A RefSeqGene (LRG_15) NG_009268.1:g.95314_95315= NG_009268.1:g.95314_95315del
UBE3A transcript variant 2 NM_000462.3:c.2363+5686= NM_000462.3:c.2363+5685_2363+5686del
UBE3A transcript variant 2 NM_000462.5:c.2363+5686= NM_000462.5:c.2363+5685_2363+5686del
UBE3A transcript variant 4 NM_001354505.1:c.2354+5686= NM_001354505.1:c.2354+5685_2354+5686del
UBE3A transcript variant 5 NM_001354506.2:c.2294+5686= NM_001354506.2:c.2294+5685_2294+5686del
UBE3A transcript variant 6 NM_001354507.2:c.2294+5686= NM_001354507.2:c.2294+5685_2294+5686del
UBE3A transcript variant 7 NM_001354508.2:c.2294+5686= NM_001354508.2:c.2294+5685_2294+5686del
UBE3A transcript variant 8 NM_001354509.2:c.2294+5686= NM_001354509.2:c.2294+5685_2294+5686del
UBE3A transcript variant 10 NM_001354511.2:c.2294+5686= NM_001354511.2:c.2294+5685_2294+5686del
UBE3A transcript variant 11 NM_001354512.2:c.2294+5686= NM_001354512.2:c.2294+5685_2294+5686del
UBE3A transcript variant 12 NM_001354513.2:c.2294+5686= NM_001354513.2:c.2294+5685_2294+5686del
UBE3A transcript variant 9 NM_001354523.2:c.2294+5686= NM_001354523.2:c.2294+5685_2294+5686del
UBE3A transcript variant 13 NM_001354526.1:c.2294+5686= NM_001354526.1:c.2294+5685_2294+5686del
UBE3A transcript variant 14 NM_001354538.2:c.2354+5686= NM_001354538.2:c.2354+5685_2354+5686del
UBE3A transcript variant 15 NM_001354539.2:c.2294+5686= NM_001354539.2:c.2294+5685_2294+5686del
UBE3A transcript variant 16 NM_001354540.2:c.2294+5686= NM_001354540.2:c.2294+5685_2294+5686del
UBE3A transcript variant 17 NM_001354541.2:c.2294+5686= NM_001354541.2:c.2294+5685_2294+5686del
UBE3A transcript variant 18 NM_001354542.2:c.2294+5686= NM_001354542.2:c.2294+5685_2294+5686del
UBE3A transcript variant 19 NM_001354543.2:c.2294+5686= NM_001354543.2:c.2294+5685_2294+5686del
UBE3A transcript variant 20 NM_001354544.2:c.2294+5686= NM_001354544.2:c.2294+5685_2294+5686del
UBE3A transcript variant 21 NM_001354545.2:c.2198+5686= NM_001354545.2:c.2198+5685_2198+5686del
UBE3A transcript variant 22 NM_001354546.2:c.2177+5686= NM_001354546.2:c.2177+5685_2177+5686del
UBE3A transcript variant 23 NM_001354547.2:c.2138+5686= NM_001354547.2:c.2138+5685_2138+5686del
UBE3A transcript variant 24 NM_001354548.2:c.2138+5686= NM_001354548.2:c.2138+5685_2138+5686del
UBE3A transcript variant 25 NM_001354549.2:c.2129+5686= NM_001354549.2:c.2129+5685_2129+5686del
UBE3A transcript variant 26 NM_001354550.2:c.1103+5686= NM_001354550.2:c.1103+5685_1103+5686del
UBE3A transcript variant 27 NM_001354551.2:c.1043+5686= NM_001354551.2:c.1043+5685_1043+5686del
UBE3A transcript variant 29 NM_001374461.1:c.2294+5686= NM_001374461.1:c.2294+5685_2294+5686del
UBE3A transcript variant 1 NM_130838.1:c.2294+5686= NM_130838.1:c.2294+5685_2294+5686del
UBE3A transcript variant 1 NM_130838.4:c.2294+5686= NM_130838.4:c.2294+5685_2294+5686del
UBE3A transcript variant 3 NM_130839.2:c.2354+5686= NM_130839.2:c.2354+5685_2354+5686del
UBE3A transcript variant 3 NM_130839.5:c.2354+5686= NM_130839.5:c.2354+5685_2354+5686del
UBE3A transcript variant X1 XM_005268267.1:c.2294+5686= XM_005268267.1:c.2294+5685_2294+5686del
UBE3A transcript variant X2 XM_005268268.1:c.2294+5686= XM_005268268.1:c.2294+5685_2294+5686del
UBE3A transcript variant X3 XM_005268269.1:c.2294+5686= XM_005268269.1:c.2294+5685_2294+5686del
UBE3A transcript variant X4 XM_005268270.1:c.2294+5686= XM_005268270.1:c.2294+5685_2294+5686del
UBE3A transcript variant X5 XM_005268271.1:c.2294+5686= XM_005268271.1:c.2294+5685_2294+5686del
UBE3A transcript variant X3 XM_011521995.4:c.2363+5686= XM_011521995.4:c.2363+5685_2363+5686del
UBE3A transcript variant X7 XM_017022547.3:c.2354+5686= XM_017022547.3:c.2354+5685_2354+5686del
UBE3A transcript variant X10 XM_017022548.3:c.2354+5686= XM_017022548.3:c.2354+5685_2354+5686del
UBE3A transcript variant X14 XM_017022550.3:c.2354+5686= XM_017022550.3:c.2354+5685_2354+5686del
UBE3A transcript variant X2 XM_024450043.2:c.2363+5686= XM_024450043.2:c.2363+5685_2363+5686del
UBE3A transcript variant X1 XM_047433007.1:c.2363+5686= XM_047433007.1:c.2363+5685_2363+5686del
UBE3A transcript variant X4 XM_047433008.1:c.2363+5686= XM_047433008.1:c.2363+5685_2363+5686del
UBE3A transcript variant X5 XM_047433009.1:c.2363+5686= XM_047433009.1:c.2363+5685_2363+5686del
UBE3A transcript variant X6 XM_047433010.1:c.2363+5686= XM_047433010.1:c.2363+5685_2363+5686del
UBE3A transcript variant X8 XM_047433011.1:c.2354+5686= XM_047433011.1:c.2354+5685_2354+5686del
UBE3A transcript variant X9 XM_047433012.1:c.2354+5686= XM_047433012.1:c.2354+5685_2354+5686del
UBE3A transcript variant X11 XM_047433013.1:c.2354+5686= XM_047433013.1:c.2354+5685_2354+5686del
UBE3A transcript variant X12 XM_047433014.1:c.2354+5686= XM_047433014.1:c.2354+5685_2354+5686del
UBE3A transcript variant X13 XM_047433015.1:c.2354+5686= XM_047433015.1:c.2354+5685_2354+5686del
UBE3A transcript variant X15 XM_047433016.1:c.2294+5686= XM_047433016.1:c.2294+5685_2294+5686del
UBE3A transcript variant X16 XM_047433017.1:c.2294+5686= XM_047433017.1:c.2294+5685_2294+5686del
UBE3A transcript variant X17 XM_047433018.1:c.2294+5686= XM_047433018.1:c.2294+5685_2294+5686del
UBE3A transcript variant X18 XM_047433019.1:c.2294+5686= XM_047433019.1:c.2294+5685_2294+5686del
UBE3A transcript variant X19 XM_047433020.1:c.2207+5686= XM_047433020.1:c.2207+5685_2207+5686del
UBE3A transcript variant X20 XM_047433021.1:c.2198+5686= XM_047433021.1:c.2198+5685_2198+5686del
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 ss2932764121 Jan 10, 2018 (151)
2 TOPMED ss4985033267 Apr 27, 2021 (155)
3 gnomAD - Genomes NC_000015.10 - 25348667 Apr 27, 2021 (155)
4 TopMed NC_000015.10 - 25348667 Apr 27, 2021 (155)
5 ALFA NC_000015.10 - 25348667 Apr 27, 2021 (155)
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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
ss2932764121 NC_000015.9:25593813:AA: NC_000015.10:25348666:AA: (self)
463705767, 200578927, 13323654541, ss4985033267 NC_000015.10:25348666:AA: NC_000015.10:25348666:AA: (self)
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Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs1491559772

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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
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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