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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.

rs147259754

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr11:72238140 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000249 (66/264690, TOPMED)
C=0.000240 (54/224618, GnomAD_exome)
C=0.000264 (37/140274, GnomAD) (+ 6 more)
C=0.000380 (39/102570, ExAC)
C=0.00030 (9/30000, ALFA)
C=0.00039 (5/12972, GO-ESP)
C=0.0003 (2/6404, 1000G_30x)
C=0.0002 (1/5008, 1000G)
C=0.0009 (4/4480, Estonian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
INPPL1 : 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 30000 G=0.99970 C=0.00030
European Sub 22198 G=0.99964 C=0.00036
African Sub 3492 G=1.0000 C=0.0000
African Others Sub 122 G=1.000 C=0.000
African American Sub 3370 G=1.0000 C=0.0000
Asian Sub 168 G=1.000 C=0.000
East Asian Sub 112 G=1.000 C=0.000
Other Asian Sub 56 G=1.00 C=0.00
Latin American 1 Sub 146 G=1.000 C=0.000
Latin American 2 Sub 610 G=1.000 C=0.000
South Asian Sub 98 G=1.00 C=0.00
Other Sub 3288 G=0.9997 C=0.0003


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=0.999751 C=0.000249
gnomAD - Exomes Global Study-wide 224618 G=0.999760 C=0.000240
gnomAD - Exomes European Sub 120912 G=0.999595 C=0.000405
gnomAD - Exomes Asian Sub 43658 G=1.00000 C=0.00000
gnomAD - Exomes American Sub 31384 G=0.99994 C=0.00006
gnomAD - Exomes African Sub 15478 G=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 7802 G=0.9999 C=0.0001
gnomAD - Exomes Other Sub 5384 G=0.9996 C=0.0004
gnomAD - Genomes Global Study-wide 140274 G=0.999736 C=0.000264
gnomAD - Genomes European Sub 75948 G=0.99955 C=0.00045
gnomAD - Genomes African Sub 42056 G=0.99998 C=0.00002
gnomAD - Genomes American Sub 13658 G=0.99985 C=0.00015
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 C=0.0000
ExAC Global Study-wide 102570 G=0.999620 C=0.000380
ExAC Europe Sub 64312 G=0.99941 C=0.00059
ExAC Asian Sub 18102 G=1.00000 C=0.00000
ExAC American Sub 10440 G=0.99990 C=0.00010
ExAC African Sub 9014 G=1.0000 C=0.0000
ExAC Other Sub 702 G=1.000 C=0.000
Allele Frequency Aggregator Total Global 30000 G=0.99970 C=0.00030
Allele Frequency Aggregator European Sub 22198 G=0.99964 C=0.00036
Allele Frequency Aggregator African Sub 3492 G=1.0000 C=0.0000
Allele Frequency Aggregator Other Sub 3288 G=0.9997 C=0.0003
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 168 G=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 C=0.00
GO Exome Sequencing Project Global Study-wide 12972 G=0.99961 C=0.00039
GO Exome Sequencing Project European American Sub 8578 G=0.9994 C=0.0006
GO Exome Sequencing Project African American Sub 4394 G=1.0000 C=0.0000
1000Genomes_30x Global Study-wide 6404 G=0.9997 C=0.0003
1000Genomes_30x African Sub 1786 G=1.0000 C=0.0000
1000Genomes_30x Europe Sub 1266 G=0.9984 C=0.0016
1000Genomes_30x South Asian Sub 1202 G=1.0000 C=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 C=0.0000
1000Genomes_30x American Sub 980 G=1.000 C=0.000
1000Genomes Global Study-wide 5008 G=0.9998 C=0.0002
1000Genomes African Sub 1322 G=1.0000 C=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 C=0.0000
1000Genomes Europe Sub 1006 G=0.9990 C=0.0010
1000Genomes South Asian Sub 978 G=1.000 C=0.000
1000Genomes American Sub 694 G=1.000 C=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9991 C=0.0009
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 11 NC_000011.10:g.72238140G>C
GRCh37.p13 chr 11 NC_000011.9:g.71949184G>C
INPPL1 RefSeqGene NG_023253.2:g.18303G>C
PHOX2A RefSeqGene NG_008169.1:g.11037C>G
Gene: INPPL1, inositol polyphosphate phosphatase like 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
INPPL1 transcript NM_001567.4:c.3651G>C L [CTG] > L [CTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 NP_001558.3:p.Leu1217= L (Leu) > L (Leu) Synonymous Variant
INPPL1 transcript variant X7 XM_047426891.1:c.3619-123…

XM_047426891.1:c.3619-123G>C

 		N/A Intron Variant
INPPL1 transcript variant X8 XM_047426892.1:c.3553-123…

XM_047426892.1:c.3553-123G>C

 		N/A Intron Variant
INPPL1 transcript variant X1 XM_005273979.5:c.3717G>C L [CTG] > L [CTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X1 XP_005274036.1:p.Leu1239= L (Leu) > L (Leu) Synonymous Variant
INPPL1 transcript variant X2 XM_047426887.1:c.3717G>C L [CTG] > L [CTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X1 XP_047282843.1:p.Leu1239= L (Leu) > L (Leu) Synonymous Variant
INPPL1 transcript variant X3 XM_047426888.1:c.3717G>C L [CTG] > L [CTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X1 XP_047282844.1:p.Leu1239= L (Leu) > L (Leu) Synonymous Variant
INPPL1 transcript variant X4 XM_047426889.1:c.3717G>C L [CTG] > L [CTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X1 XP_047282845.1:p.Leu1239= L (Leu) > L (Leu) Synonymous Variant
INPPL1 transcript variant X5 XM_011544999.3:c.3651G>C L [CTG] > L [CTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X2 XP_011543301.1:p.Leu1217= L (Leu) > L (Leu) Synonymous Variant
INPPL1 transcript variant X6 XM_047426890.1:c.3651G>C L [CTG] > L [CTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X2 XP_047282846.1:p.Leu1217= L (Leu) > L (Leu) Synonymous Variant
INPPL1 transcript variant X9 XM_047426893.1:c.3354G>C L [CTG] > L [CTC] Coding Sequence Variant
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X5 XP_047282849.1:p.Leu1118= 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.

Allele: C (allele ID: 713147 )
ClinVar Accession Disease Names Clinical Significance
RCV000973198.4 not provided Likely-Benign
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= C
GRCh38.p14 chr 11 NC_000011.10:g.72238140= NC_000011.10:g.72238140G>C
GRCh37.p13 chr 11 NC_000011.9:g.71949184= NC_000011.9:g.71949184G>C
INPPL1 RefSeqGene NG_023253.2:g.18303= NG_023253.2:g.18303G>C
INPPL1 transcript NM_001567.4:c.3651= NM_001567.4:c.3651G>C
INPPL1 transcript NM_001567.3:c.3651= NM_001567.3:c.3651G>C
PHOX2A RefSeqGene NG_008169.1:g.11037= NG_008169.1:g.11037C>G
INPPL1 transcript variant X1 XM_005273979.5:c.3717= XM_005273979.5:c.3717G>C
INPPL1 transcript variant X5 XM_005273979.4:c.3717= XM_005273979.4:c.3717G>C
INPPL1 transcript variant X1 XM_005273979.3:c.3717= XM_005273979.3:c.3717G>C
INPPL1 transcript variant X2 XM_005273979.2:c.3717= XM_005273979.2:c.3717G>C
INPPL1 transcript variant X2 XM_005273979.1:c.3717= XM_005273979.1:c.3717G>C
INPPL1 transcript variant X5 XM_011544999.3:c.3651= XM_011544999.3:c.3651G>C
INPPL1 transcript variant X6 XM_011544999.2:c.3651= XM_011544999.2:c.3651G>C
INPPL1 transcript variant X3 XM_011544999.1:c.3651= XM_011544999.1:c.3651G>C
INPPL1 transcript variant X4 XM_047426889.1:c.3717= XM_047426889.1:c.3717G>C
INPPL1 transcript variant X2 XM_047426887.1:c.3717= XM_047426887.1:c.3717G>C
INPPL1 transcript variant X3 XM_047426888.1:c.3717= XM_047426888.1:c.3717G>C
INPPL1 transcript variant X6 XM_047426890.1:c.3651= XM_047426890.1:c.3651G>C
INPPL1 transcript variant X9 XM_047426893.1:c.3354= XM_047426893.1:c.3354G>C
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 NP_001558.3:p.Leu1217= NP_001558.3:p.Leu1217=
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X1 XP_005274036.1:p.Leu1239= XP_005274036.1:p.Leu1239=
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X2 XP_011543301.1:p.Leu1217= XP_011543301.1:p.Leu1217=
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X1 XP_047282845.1:p.Leu1239= XP_047282845.1:p.Leu1239=
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X1 XP_047282843.1:p.Leu1239= XP_047282843.1:p.Leu1239=
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X1 XP_047282844.1:p.Leu1239= XP_047282844.1:p.Leu1239=
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X2 XP_047282846.1:p.Leu1217= XP_047282846.1:p.Leu1217=
phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 2 isoform X5 XP_047282849.1:p.Leu1118= XP_047282849.1:p.Leu1118=
INPPL1 transcript variant X3 XM_005273980.1:c.3619-123= XM_005273980.1:c.3619-123G>C
INPPL1 transcript variant X7 XM_047426891.1:c.3619-123= XM_047426891.1:c.3619-123G>C
INPPL1 transcript variant X8 XM_047426892.1:c.3553-123= XM_047426892.1:c.3553-123G>C
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#.

17 SubSNP, 9 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342335412 May 09, 2011 (134)
2 1000GENOMES ss1341834396 Aug 21, 2014 (142)
3 EVA_EXAC ss1690533006 Apr 01, 2015 (144)
4 HUMAN_LONGEVITY ss2183433497 Dec 20, 2016 (150)
5 GNOMAD ss2739227219 Nov 08, 2017 (151)
6 GNOMAD ss2748690552 Nov 08, 2017 (151)
7 GNOMAD ss2901262274 Nov 08, 2017 (151)
8 EGCUT_WGS ss3675645029 Jul 13, 2019 (153)
9 EVA ss3824650957 Apr 26, 2020 (154)
10 EVA ss3986536887 Apr 26, 2021 (155)
11 TOPMED ss4890093015 Apr 26, 2021 (155)
12 1000G_HIGH_COVERAGE ss5287918339 Oct 16, 2022 (156)
13 EVA ss5400460123 Oct 16, 2022 (156)
14 HUGCELL_USP ss5483026452 Oct 16, 2022 (156)
15 1000G_HIGH_COVERAGE ss5583883698 Oct 16, 2022 (156)
16 EVA ss5836849756 Oct 16, 2022 (156)
17 EVA ss5920528490 Oct 16, 2022 (156)
18 1000Genomes NC_000011.9 - 71949184 Oct 12, 2018 (152)
19 1000Genomes_30x NC_000011.10 - 72238140 Oct 16, 2022 (156)
20 Genetic variation in the Estonian population NC_000011.9 - 71949184 Oct 12, 2018 (152)
21 ExAC NC_000011.9 - 71949184 Oct 12, 2018 (152)
22 gnomAD - Genomes NC_000011.10 - 72238140 Apr 26, 2021 (155)
23 gnomAD - Exomes NC_000011.9 - 71949184 Jul 13, 2019 (153)
24 GO Exome Sequencing Project NC_000011.9 - 71949184 Oct 12, 2018 (152)
25 TopMed NC_000011.10 - 72238140 Apr 26, 2021 (155)
26 ALFA NC_000011.10 - 72238140 Apr 26, 2021 (155)
27 ClinVar RCV000973198.4 Oct 16, 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
54375464, 21383277, 800776, 8443996, 1108524, ss342335412, ss1341834396, ss1690533006, ss2739227219, ss2748690552, ss2901262274, ss3675645029, ss3824650957, ss3986536887, ss5400460123, ss5836849756 NC_000011.9:71949183:G:C NC_000011.10:72238139:G:C (self)
RCV000973198.4, 71409633, 383807096, 105638671, 11561878004, ss2183433497, ss4890093015, ss5287918339, ss5483026452, ss5583883698, ss5920528490 NC_000011.10:72238139:G:C NC_000011.10:72238139:G:C (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 rs147259754

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