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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.

rs148239915

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:94298373 (GRCh38.p13) 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 / G>C / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00004 (1/23038, ALFA)
T=0.00008 (1/11830, GO-ESP)
C=0.0016 (8/5008, 1000G) (+ 1 more)
T=0.005 (1/216, Qatari)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PLCE1 : Intron Variant
Publications
0 citations
Genomic View
See rs on genome
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.p13 chr 10 NC_000010.11:g.94298373G>A
GRCh38.p13 chr 10 NC_000010.11:g.94298373G>C
GRCh38.p13 chr 10 NC_000010.11:g.94298373G>T
GRCh37.p13 chr 10 NC_000010.10:g.96058130G>A
GRCh37.p13 chr 10 NC_000010.10:g.96058130G>C
GRCh37.p13 chr 10 NC_000010.10:g.96058130G>T
PLCE1 RefSeqGene NG_015799.1:g.309385G>A
PLCE1 RefSeqGene NG_015799.1:g.309385G>C
PLCE1 RefSeqGene NG_015799.1:g.309385G>T
Gene: PLCE1, phospholipase C epsilon 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PLCE1 transcript variant 2 NM_001165979.2:c.4244-6G>A N/A Intron Variant
PLCE1 transcript variant 3 NM_001288989.2:c.5120-6G>A N/A Intron Variant
PLCE1 transcript variant 1 NM_016341.4:c.5168-6G>A N/A Intron Variant
PLCE1 transcript variant X1 XM_006717885.4:c.5210-6G>A N/A Intron Variant
PLCE1 transcript variant X5 XM_006717888.4:c.5207-6G>A N/A Intron Variant
PLCE1 transcript variant X6 XM_006717889.4:c.5162-6G>A N/A Intron Variant
PLCE1 transcript variant X7 XM_006717890.3:c.4286-6G>A N/A Intron Variant
PLCE1 transcript variant X2 XM_011539849.3:c.5210-6G>A N/A Intron Variant
PLCE1 transcript variant X9 XM_011539850.3:c.4055-6G>A N/A Intron Variant
PLCE1 transcript variant X3 XM_017016310.2:c.5210-6G>A N/A Intron Variant
PLCE1 transcript variant X4 XM_017016311.2:c.5210-6G>A N/A Intron Variant
PLCE1 transcript variant X8 XM_017016312.2:c.4196-6G>A N/A Intron Variant
PLCE1 transcript variant X10 XM_011539851.3:c. N/A Genic Downstream Transcript Variant
PLCE1 transcript variant X11 XM_011539852.3:c. N/A Genic Downstream Transcript 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: 868542 )
ClinVar Accession Disease Names Clinical Significance
RCV001106876.1 Nephrotic syndrome, type 3 Likely-Benign
Allele: T (allele ID: 311768 )
ClinVar Accession Disease Names Clinical Significance
RCV000355722.2 Nephrotic syndrome, type 3 Uncertain-Significance
RCV000980371.1 not provided Likely-Benign

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 23038 G=0.99996 C=0.00000, T=0.00004
European Sub 15752 G=0.99994 C=0.00000, T=0.00006
African Sub 3492 G=1.0000 C=0.0000, T=0.0000
African Others Sub 122 G=1.000 C=0.000, T=0.000
African American Sub 3370 G=1.0000 C=0.0000, T=0.0000
Asian Sub 168 G=1.000 C=0.000, T=0.000
East Asian Sub 112 G=1.000 C=0.000, T=0.000
Other Asian Sub 56 G=1.00 C=0.00, T=0.00
Latin American 1 Sub 146 G=1.000 C=0.000, T=0.000
Latin American 2 Sub 610 G=1.000 C=0.000, T=0.000
South Asian Sub 98 G=1.00 C=0.00, T=0.00
Other Sub 2772 G=1.0000 C=0.0000, T=0.0000


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
GO Exome Sequencing Project Global Study-wide 11830 G=0.99992 T=0.00008
GO Exome Sequencing Project European American Sub 8172 G=0.9999 T=0.0001
GO Exome Sequencing Project African American Sub 3658 G=1.0000 T=0.0000
1000Genomes Global Study-wide 5008 G=0.9984 C=0.0016
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=1.0000 C=0.0000
1000Genomes South Asian Sub 978 G=0.992 C=0.008
1000Genomes American Sub 694 G=1.000 C=0.000
Qatari Global Study-wide 216 G=0.995 T=0.005
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 C T
GRCh38.p13 chr 10 NC_000010.11:g.94298373= NC_000010.11:g.94298373G>A NC_000010.11:g.94298373G>C NC_000010.11:g.94298373G>T
GRCh37.p13 chr 10 NC_000010.10:g.96058130= NC_000010.10:g.96058130G>A NC_000010.10:g.96058130G>C NC_000010.10:g.96058130G>T
PLCE1 RefSeqGene NG_015799.1:g.309385= NG_015799.1:g.309385G>A NG_015799.1:g.309385G>C NG_015799.1:g.309385G>T
PLCE1 transcript variant 2 NM_001165979.1:c.4244-6= NM_001165979.1:c.4244-6G>A NM_001165979.1:c.4244-6G>C NM_001165979.1:c.4244-6G>T
PLCE1 transcript variant 2 NM_001165979.2:c.4244-6= NM_001165979.2:c.4244-6G>A NM_001165979.2:c.4244-6G>C NM_001165979.2:c.4244-6G>T
PLCE1 transcript variant 3 NM_001288989.2:c.5120-6= NM_001288989.2:c.5120-6G>A NM_001288989.2:c.5120-6G>C NM_001288989.2:c.5120-6G>T
PLCE1 transcript variant 1 NM_016341.3:c.5168-6= NM_016341.3:c.5168-6G>A NM_016341.3:c.5168-6G>C NM_016341.3:c.5168-6G>T
PLCE1 transcript variant 1 NM_016341.4:c.5168-6= NM_016341.4:c.5168-6G>A NM_016341.4:c.5168-6G>C NM_016341.4:c.5168-6G>T
PLCE1 transcript variant X1 XM_005269880.1:c.5168-6= XM_005269880.1:c.5168-6G>A XM_005269880.1:c.5168-6G>C XM_005269880.1:c.5168-6G>T
PLCE1 transcript variant X2 XM_005269881.1:c.5120-6= XM_005269881.1:c.5120-6G>A XM_005269881.1:c.5120-6G>C XM_005269881.1:c.5120-6G>T
PLCE1 transcript variant X3 XM_005269882.1:c.2333-6= XM_005269882.1:c.2333-6G>A XM_005269882.1:c.2333-6G>C XM_005269882.1:c.2333-6G>T
PLCE1 transcript variant X1 XM_006717885.4:c.5210-6= XM_006717885.4:c.5210-6G>A XM_006717885.4:c.5210-6G>C XM_006717885.4:c.5210-6G>T
PLCE1 transcript variant X5 XM_006717888.4:c.5207-6= XM_006717888.4:c.5207-6G>A XM_006717888.4:c.5207-6G>C XM_006717888.4:c.5207-6G>T
PLCE1 transcript variant X6 XM_006717889.4:c.5162-6= XM_006717889.4:c.5162-6G>A XM_006717889.4:c.5162-6G>C XM_006717889.4:c.5162-6G>T
PLCE1 transcript variant X7 XM_006717890.3:c.4286-6= XM_006717890.3:c.4286-6G>A XM_006717890.3:c.4286-6G>C XM_006717890.3:c.4286-6G>T
PLCE1 transcript variant X2 XM_011539849.3:c.5210-6= XM_011539849.3:c.5210-6G>A XM_011539849.3:c.5210-6G>C XM_011539849.3:c.5210-6G>T
PLCE1 transcript variant X9 XM_011539850.3:c.4055-6= XM_011539850.3:c.4055-6G>A XM_011539850.3:c.4055-6G>C XM_011539850.3:c.4055-6G>T
PLCE1 transcript variant X3 XM_017016310.2:c.5210-6= XM_017016310.2:c.5210-6G>A XM_017016310.2:c.5210-6G>C XM_017016310.2:c.5210-6G>T
PLCE1 transcript variant X4 XM_017016311.2:c.5210-6= XM_017016311.2:c.5210-6G>A XM_017016311.2:c.5210-6G>C XM_017016311.2:c.5210-6G>T
PLCE1 transcript variant X8 XM_017016312.2:c.4196-6= XM_017016312.2:c.4196-6G>A XM_017016312.2:c.4196-6G>C XM_017016312.2:c.4196-6G>T
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, 14 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss336315684 May 09, 2011 (134)
2 1000GENOMES ss491001470 May 04, 2012 (137)
3 NHLBI-ESP ss712959829 Apr 25, 2013 (138)
4 1000GENOMES ss1338609899 Aug 21, 2014 (142)
5 EVA_EXAC ss1690008992 Apr 01, 2015 (144)
6 EVA_EXAC ss1690008993 Apr 01, 2015 (144)
7 EVA_EXAC ss1690008994 Apr 01, 2015 (144)
8 WEILL_CORNELL_DGM ss1931167100 Feb 12, 2016 (147)
9 HUMAN_LONGEVITY ss2177121368 Dec 20, 2016 (150)
10 TOPMED ss2340232132 Dec 20, 2016 (150)
11 GNOMAD ss2738416257 Nov 08, 2017 (151)
12 TOPMED ss3127431411 Nov 08, 2017 (151)
13 EVA ss3824540340 Apr 26, 2020 (154)
14 GNOMAD ss4223571848 Apr 27, 2021 (155)
15 GNOMAD ss4223571849 Apr 27, 2021 (155)
16 TOPMED ss4862508974 Apr 27, 2021 (155)
17 TOPMED ss4862508975 Apr 27, 2021 (155)
18 1000Genomes NC_000010.10 - 96058130 Oct 12, 2018 (152)
19 ExAC

Submission ignored due to conflicting rows:
Row 238347 (NC_000010.10:96058129:G:G 120448/120500, NC_000010.10:96058129:G:C 52/120500)
Row 238348 (NC_000010.10:96058129:G:G 120499/120500, NC_000010.10:96058129:G:A 1/120500)
Row 238349 (NC_000010.10:96058129:G:G 120497/120500, NC_000010.10:96058129:G:T 3/120500)

- Oct 12, 2018 (152)
20 ExAC

Submission ignored due to conflicting rows:
Row 238347 (NC_000010.10:96058129:G:G 120448/120500, NC_000010.10:96058129:G:C 52/120500)
Row 238348 (NC_000010.10:96058129:G:G 120499/120500, NC_000010.10:96058129:G:A 1/120500)
Row 238349 (NC_000010.10:96058129:G:G 120497/120500, NC_000010.10:96058129:G:T 3/120500)

- Oct 12, 2018 (152)
21 ExAC

Submission ignored due to conflicting rows:
Row 238347 (NC_000010.10:96058129:G:G 120448/120500, NC_000010.10:96058129:G:C 52/120500)
Row 238348 (NC_000010.10:96058129:G:G 120499/120500, NC_000010.10:96058129:G:A 1/120500)
Row 238349 (NC_000010.10:96058129:G:G 120497/120500, NC_000010.10:96058129:G:T 3/120500)

- Oct 12, 2018 (152)
22 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 360639328 (NC_000010.11:94298372:G:C 0/140154)
Row 360639329 (NC_000010.11:94298372:G:T 3/140154)

- Apr 27, 2021 (155)
23 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 360639328 (NC_000010.11:94298372:G:C 0/140154)
Row 360639329 (NC_000010.11:94298372:G:T 3/140154)

- Apr 27, 2021 (155)
24 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 7615947 (NC_000010.10:96058129:G:G 249122/249124, NC_000010.10:96058129:G:A 2/249124)
Row 7615948 (NC_000010.10:96058129:G:G 249046/249124, NC_000010.10:96058129:G:C 78/249124)
Row 7615949 (NC_000010.10:96058129:G:G 249121/249124, NC_000010.10:96058129:G:T 3/249124)

- Jul 13, 2019 (153)
25 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 7615947 (NC_000010.10:96058129:G:G 249122/249124, NC_000010.10:96058129:G:A 2/249124)
Row 7615948 (NC_000010.10:96058129:G:G 249046/249124, NC_000010.10:96058129:G:C 78/249124)
Row 7615949 (NC_000010.10:96058129:G:G 249121/249124, NC_000010.10:96058129:G:T 3/249124)

- Jul 13, 2019 (153)
26 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 7615947 (NC_000010.10:96058129:G:G 249122/249124, NC_000010.10:96058129:G:A 2/249124)
Row 7615948 (NC_000010.10:96058129:G:G 249046/249124, NC_000010.10:96058129:G:C 78/249124)
Row 7615949 (NC_000010.10:96058129:G:G 249121/249124, NC_000010.10:96058129:G:T 3/249124)

- Jul 13, 2019 (153)
27 GO Exome Sequencing Project NC_000010.10 - 96058130 Oct 12, 2018 (152)
28 Qatari NC_000010.10 - 96058130 Apr 26, 2020 (154)
29 TopMed

Submission ignored due to conflicting rows:
Row 78054629 (NC_000010.11:94298372:G:C 4/264690)
Row 78054630 (NC_000010.11:94298372:G:T 1/264690)

- Apr 27, 2021 (155)
30 TopMed

Submission ignored due to conflicting rows:
Row 78054629 (NC_000010.11:94298372:G:C 4/264690)
Row 78054630 (NC_000010.11:94298372:G:T 1/264690)

- Apr 27, 2021 (155)
31 ALFA NC_000010.11 - 94298373 Apr 27, 2021 (155)
32 ClinVar RCV000355722.2 Apr 27, 2021 (155)
33 ClinVar RCV000980371.1 Apr 26, 2020 (154)
34 ClinVar RCV001106876.1 Apr 27, 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
ss1690008993, ss2738416257 NC_000010.10:96058129:G:A NC_000010.11:94298372:G:A (self)
51040803, ss1338609899, ss1690008992, ss2340232132, ss2738416257 NC_000010.10:96058129:G:C NC_000010.11:94298372:G:C (self)
RCV001106876.1, 49071019, 7906154958, ss2177121368, ss3127431411, ss4223571848, ss4862508974 NC_000010.11:94298372:G:C NC_000010.11:94298372:G:C (self)
998024, 13209030, ss336315684, ss491001470, ss712959829, ss1690008994, ss1931167100, ss2738416257, ss3824540340 NC_000010.10:96058129:G:T NC_000010.11:94298372:G:T (self)
RCV000355722.2, RCV000980371.1, 7906154958, ss4223571849, ss4862508975 NC_000010.11:94298372:G:T NC_000010.11:94298372:G:T (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 rs148239915

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.post596+ae089ad