Name: rs540224444
Published: September 21, 2022
License: Open Access

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.

rs540224444

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr12:18645564 (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=0.000011 (3/264690, TOPMED)
C=0.000178 (25/140208, GnomAD)
C=0.00018 (3/16332, ALFA) (+ 6 more)
C=0.0002 (1/6404, 1000G_30x)
C=0.0002 (1/5008, 1000G)
C=0.0007 (3/4480, Estonian)
C=0.002 (1/600, NorthernSweden)
G=0.5 (1/2, Siberian)
C=0.5 (1/2, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PIK3C2G : Intron Variant
PLCZ1 : 500B Downstream 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	16332	G=0.99982	C=0.00018
European	Sub	12080	G=0.99975	C=0.00025
African	Sub	2816	G=1.0000	C=0.0000
African Others	Sub	108	G=1.000	C=0.000
African American	Sub	2708	G=1.0000	C=0.0000
Asian	Sub	108	G=1.000	C=0.000
East Asian	Sub	84	G=1.00	C=0.00
Other Asian	Sub	24	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	94	G=1.00	C=0.00
Other	Sub	478	G=1.000	C=0.000

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.999989	C=0.000011
gnomAD - Genomes	Global	Study-wide	140208	G=0.999822	C=0.000178
gnomAD - Genomes	European	Sub	75932	G=0.99968	C=0.00032
gnomAD - Genomes	African	Sub	42020	G=0.99998	C=0.00002
gnomAD - Genomes	American	Sub	13650	G=1.00000	C=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=1.0000	C=0.0000
gnomAD - Genomes	East Asian	Sub	3134	G=1.0000	C=0.0000
gnomAD - Genomes	Other	Sub	2152	G=1.0000	C=0.0000
Allele Frequency Aggregator	Total	Global	16332	G=0.99982	C=0.00018
Allele Frequency Aggregator	European	Sub	12080	G=0.99975	C=0.00025
Allele Frequency Aggregator	African	Sub	2816	G=1.0000	C=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	610	G=1.000	C=0.000
Allele Frequency Aggregator	Other	Sub	478	G=1.000	C=0.000
Allele Frequency Aggregator	Latin American 1	Sub	146	G=1.000	C=0.000
Allele Frequency Aggregator	Asian	Sub	108	G=1.000	C=0.000
Allele Frequency Aggregator	South Asian	Sub	94	G=1.00	C=0.00
1000Genomes_30x	Global	Study-wide	6404	G=0.9998	C=0.0002
1000Genomes_30x	African	Sub	1786	G=1.0000	C=0.0000
1000Genomes_30x	Europe	Sub	1266	G=0.9992	C=0.0008
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=0.9993	C=0.0007
Northern Sweden	ACPOP	Study-wide	600	G=0.998	C=0.002
Siberian	Global	Study-wide	2	G=0.5	C=0.5

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 12	NC_000012.12:g.18645564G>C
GRCh37.p13 chr 12	NC_000012.11:g.18798498G>C
PIK3C2G RefSeqGene	NG_050635.1:g.407600G>C
PLCZ1 RefSeqGene	NG_052826.1:g.97496C>G

Gene: PIK3C2G, phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 gamma (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PIK3C2G transcript variant 1	NM_001288772.2:c.4309-231… NM_001288772.2:c.4309-2312G>C	N/A	Intron Variant
PIK3C2G transcript variant 2	NM_001288774.2:c.3643-231… NM_001288774.2:c.3643-2312G>C	N/A	Intron Variant
PIK3C2G transcript variant 3	NM_004570.6:c.4186-2312G>C	N/A	Intron Variant
PIK3C2G transcript variant X8	XM_011520697.3:c.4308+501… XM_011520697.3:c.4308+5010G>C	N/A	Intron Variant
PIK3C2G transcript variant X1	XM_017019471.2:c.4308+501… XM_017019471.2:c.4308+5010G>C	N/A	Intron Variant
PIK3C2G transcript variant X2	XM_017019473.3:c.4308+501… XM_017019473.3:c.4308+5010G>C	N/A	Intron Variant
PIK3C2G transcript variant X14	XM_017019479.2:c.2283+501… XM_017019479.2:c.2283+5010G>C	N/A	Intron Variant
PIK3C2G transcript variant X3	XM_047429005.1:c.4309-231… XM_047429005.1:c.4309-2312G>C	N/A	Intron Variant
PIK3C2G transcript variant X4	XM_047429006.1:c.4309-231… XM_047429006.1:c.4309-2312G>C	N/A	Intron Variant
PIK3C2G transcript variant X5	XM_047429007.1:c.4308+501… XM_047429007.1:c.4308+5010G>C	N/A	Intron Variant
PIK3C2G transcript variant X6	XM_047429008.1:c.4185+501… XM_047429008.1:c.4185+5010G>C	N/A	Intron Variant
PIK3C2G transcript variant X7	XM_047429009.1:c.4186-231… XM_047429009.1:c.4186-2312G>C	N/A	Intron Variant
PIK3C2G transcript variant X10	XM_047429010.1:c.3643-231… XM_047429010.1:c.3643-2312G>C	N/A	Intron Variant
PIK3C2G transcript variant X9	XM_017019475.2:c.*1908=	N/A	3 Prime UTR Variant
PIK3C2G transcript variant X12	XM_011520701.3:c.	N/A	Genic Downstream Transcript Variant
PIK3C2G transcript variant X13	XM_017019478.3:c.	N/A	Genic Downstream Transcript Variant
PIK3C2G transcript variant X11	XR_931307.3:n.	N/A	Genic Downstream Transcript Variant

Gene: PLCZ1, phospholipase C zeta 1 (minus strand) : 500B Downstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
PLCZ1 transcript variant 3	NM_001330769.1:c.	N/A	N/A
PLCZ1 transcript variant 2	NM_001330774.2:c.	N/A	N/A
PLCZ1 transcript variant 1	NM_033123.4:c.	N/A	N/A
PLCZ1 transcript variant X1	XM_017020176.2:c.	N/A	N/A
PLCZ1 transcript variant X3	XM_017020177.2:c.	N/A	N/A
PLCZ1 transcript variant X4	XM_017020178.2:c.	N/A	N/A
PLCZ1 transcript variant X6	XM_017020182.2:c.	N/A	N/A
PLCZ1 transcript variant X7	XM_017020183.2:c.	N/A	N/A
PLCZ1 transcript variant X9	XM_017020184.2:c.	N/A	N/A
PLCZ1 transcript variant X12	XM_017020185.3:c.	N/A	N/A
PLCZ1 transcript variant X8	XM_024449254.2:c.	N/A	N/A
PLCZ1 transcript variant X10	XM_024449255.2:c.	N/A	N/A
PLCZ1 transcript variant X5	XM_047429827.1:c.	N/A	N/A
PLCZ1 transcript variant X11	XM_047429828.1:c.	N/A	N/A
PLCZ1 transcript variant X2	XR_001748912.2:n.	N/A	Downstream Transcript Variant

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

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 12	NC_000012.12:g.18645564=	NC_000012.12:g.18645564G>C
GRCh37.p13 chr 12	NC_000012.11:g.18798498=	NC_000012.11:g.18798498G>C
PIK3C2G RefSeqGene	NG_050635.1:g.407600=	NG_050635.1:g.407600G>C
PLCZ1 RefSeqGene	NG_052826.1:g.97496=	NG_052826.1:g.97496C>G
PIK3C2G transcript variant X9	XM_017019475.2:c.*1908=	XM_017019475.2:c.*1908G>C
PIK3C2G transcript variant 1	NM_001288772.2:c.4309-2312=	NM_001288772.2:c.4309-2312G>C
PIK3C2G transcript variant 2	NM_001288774.2:c.3643-2312=	NM_001288774.2:c.3643-2312G>C
PIK3C2G transcript	NM_004570.4:c.4186-2312=	NM_004570.4:c.4186-2312G>C
PIK3C2G transcript variant 3	NM_004570.6:c.4186-2312=	NM_004570.6:c.4186-2312G>C
PIK3C2G transcript variant X1	XM_005253393.1:c.4309-2312=	XM_005253393.1:c.4309-2312G>C
PIK3C2G transcript variant X8	XM_011520697.3:c.4308+5010=	XM_011520697.3:c.4308+5010G>C
PIK3C2G transcript variant X1	XM_017019471.2:c.4308+5010=	XM_017019471.2:c.4308+5010G>C
PIK3C2G transcript variant X2	XM_017019473.3:c.4308+5010=	XM_017019473.3:c.4308+5010G>C
PIK3C2G transcript variant X14	XM_017019479.2:c.2283+5010=	XM_017019479.2:c.2283+5010G>C
PIK3C2G transcript variant X3	XM_047429005.1:c.4309-2312=	XM_047429005.1:c.4309-2312G>C
PIK3C2G transcript variant X4	XM_047429006.1:c.4309-2312=	XM_047429006.1:c.4309-2312G>C
PIK3C2G transcript variant X5	XM_047429007.1:c.4308+5010=	XM_047429007.1:c.4308+5010G>C
PIK3C2G transcript variant X6	XM_047429008.1:c.4185+5010=	XM_047429008.1:c.4185+5010G>C
PIK3C2G transcript variant X7	XM_047429009.1:c.4186-2312=	XM_047429009.1:c.4186-2312G>C
PIK3C2G transcript variant X10	XM_047429010.1:c.3643-2312=	XM_047429010.1:c.3643-2312G>C

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#.

11 SubSNP, 8 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss1344128504	Aug 21, 2014 (142)
2	USC_VALOUEV	ss2155401297	Dec 20, 2016 (150)
3	GNOMAD	ss2907959034	Nov 08, 2017 (151)
4	SWEGEN	ss3009297019	Nov 08, 2017 (151)
5	EGCUT_WGS	ss3676611602	Jul 13, 2019 (153)
6	ACPOP	ss3738817961	Jul 13, 2019 (153)
7	TOPMED	ss4910545338	Apr 26, 2021 (155)
8	EVA	ss5404262744	Oct 16, 2022 (156)
9	1000G_HIGH_COVERAGE	ss5587017466	Oct 16, 2022 (156)
10	SANFORD_IMAGENETICS	ss5652700389	Oct 16, 2022 (156)
11	EVA	ss5903496739	Oct 16, 2022 (156)
12	1000Genomes	NC_000012.11 - 18798498	Oct 12, 2018 (152)
13	1000Genomes_30x	NC_000012.12 - 18645564	Oct 16, 2022 (156)
14	Genetic variation in the Estonian population	NC_000012.11 - 18798498	Oct 12, 2018 (152)
15	gnomAD - Genomes	NC_000012.12 - 18645564	Apr 26, 2021 (155)
16	Northern Sweden	NC_000012.11 - 18798498	Jul 13, 2019 (153)
17	Siberian	NC_000012.11 - 18798498	Apr 26, 2020 (154)
18	TopMed	NC_000012.12 - 18645564	Apr 26, 2021 (155)
19	ALFA	NC_000012.12 - 18645564	Apr 26, 2021 (155)

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
56844203, 22349850, 12102826, 7917651, ss1344128504, ss2155401297, ss2907959034, ss3009297019, ss3676611602, ss3738817961, ss5404262744, ss5652700389	NC_000012.11:18798497:G:C	NC_000012.12:18645563:G:C	(self)
74543401, 400828030, 126090995, 5352232113, ss4910545338, ss5587017466, ss5903496739	NC_000012.12:18645563:G:C	NC_000012.12:18645563:G:C	(self)

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

No publications for rs540224444

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs540224444