Name: rs192436108
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.

rs192436108

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr2:182400293 (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: T>A
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.008202 (2171/264690, TOPMED)
A=0.008777 (1231/140258, GnomAD)
A=0.00004 (1/28256, 14KJPN) (+ 11 more)
A=0.01239 (234/18890, ALFA)
A=0.0031 (20/6404, 1000G_30x)
A=0.0028 (14/5008, 1000G)
A=0.0181 (81/4480, Estonian)
A=0.0143 (55/3854, ALSPAC)
A=0.0140 (52/3708, TWINSUK)
A=0.011 (11/998, GoNL)
A=0.007 (4/600, NorthernSweden)
A=0.03 (1/40, GENOME_DK)
T=0.5 (3/6, SGDP_PRJ)
A=0.5 (3/6, SGDP_PRJ)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PDE1A : 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18890	T=0.98761	A=0.01239
European	Sub	14286	T=0.98460	A=0.01540
African	Sub	2946	T=0.9990	A=0.0010
African Others	Sub	114	T=1.000	A=0.000
African American	Sub	2832	T=0.9989	A=0.0011
Asian	Sub	112	T=1.000	A=0.000
East Asian	Sub	86	T=1.00	A=0.00
Other Asian	Sub	26	T=1.00	A=0.00
Latin American 1	Sub	146	T=0.986	A=0.014
Latin American 2	Sub	610	T=0.995	A=0.005
South Asian	Sub	98	T=0.99	A=0.01
Other	Sub	692	T=0.993	A=0.007

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	T=0.991798	A=0.008202
gnomAD - Genomes	Global	Study-wide	140258	T=0.991223	A=0.008777
gnomAD - Genomes	European	Sub	75940	T=0.98632	A=0.01368
gnomAD - Genomes	African	Sub	42058	T=0.99788	A=0.00212
gnomAD - Genomes	American	Sub	13656	T=0.99385	A=0.00615
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	T=0.9997	A=0.0003
gnomAD - Genomes	East Asian	Sub	3130	T=1.0000	A=0.0000
gnomAD - Genomes	Other	Sub	2154	T=0.9916	A=0.0084
14KJPN	JAPANESE	Study-wide	28256	T=0.99996	A=0.00004
Allele Frequency Aggregator	Total	Global	18890	T=0.98761	A=0.01239
Allele Frequency Aggregator	European	Sub	14286	T=0.98460	A=0.01540
Allele Frequency Aggregator	African	Sub	2946	T=0.9990	A=0.0010
Allele Frequency Aggregator	Other	Sub	692	T=0.993	A=0.007
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.995	A=0.005
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.986	A=0.014
Allele Frequency Aggregator	Asian	Sub	112	T=1.000	A=0.000
Allele Frequency Aggregator	South Asian	Sub	98	T=0.99	A=0.01
1000Genomes_30x	Global	Study-wide	6404	T=0.9969	A=0.0031
1000Genomes_30x	African	Sub	1786	T=1.0000	A=0.0000
1000Genomes_30x	Europe	Sub	1266	T=0.9889	A=0.0111
1000Genomes_30x	South Asian	Sub	1202	T=1.0000	A=0.0000
1000Genomes_30x	East Asian	Sub	1170	T=0.9983	A=0.0017
1000Genomes_30x	American	Sub	980	T=0.996	A=0.004
1000Genomes	Global	Study-wide	5008	T=0.9972	A=0.0028
1000Genomes	African	Sub	1322	T=1.0000	A=0.0000
1000Genomes	East Asian	Sub	1008	T=0.9990	A=0.0010
1000Genomes	Europe	Sub	1006	T=0.9901	A=0.0099
1000Genomes	South Asian	Sub	978	T=1.000	A=0.000
1000Genomes	American	Sub	694	T=0.996	A=0.004
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.9819	A=0.0181
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.9857	A=0.0143
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.9860	A=0.0140
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.989	A=0.011
Northern Sweden	ACPOP	Study-wide	600	T=0.993	A=0.007
The Danish reference pan genome	Danish	Study-wide	40	T=0.97	A=0.03
SGDP_PRJ	Global	Study-wide	6	T=0.5	A=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 2	NC_000002.12:g.182400293T>A
GRCh37.p13 chr 2	NC_000002.11:g.183265020T>A

Gene: PDE1A, phosphodiesterase 1A (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PDE1A transcript variant 2	NM_001003683.3:c.101+1219… NM_001003683.3:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant 3	NM_001258312.3:c.113+1219… NM_001258312.3:c.113+121983A>T	N/A	Intron Variant
PDE1A transcript variant 4	NM_001258313.3:c.53+26285… NM_001258313.3:c.53+26285A>T	N/A	Intron Variant
PDE1A transcript variant 6	NM_001363871.4:c.53+26285… NM_001363871.4:c.53+26285A>T	N/A	Intron Variant
PDE1A transcript variant 7	NM_001395258.2:c.101+1219… NM_001395258.2:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant 8	NM_001395259.2:c.101+1219… NM_001395259.2:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant 9	NM_001395260.2:c.101+1219… NM_001395260.2:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant 10	NM_001395261.2:c.101+1219… NM_001395261.2:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant 11	NM_001395262.1:c.101+1219… NM_001395262.1:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant 12	NM_001395263.1:c.101+1219… NM_001395263.1:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant 13	NM_001395264.1:c.53+26285… NM_001395264.1:c.53+26285A>T	N/A	Intron Variant
PDE1A transcript variant 14	NM_001395265.2:c.-212+633… NM_001395265.2:c.-212+63305A>T	N/A	Intron Variant
PDE1A transcript variant 15	NM_001395266.1:c.101+1219… NM_001395266.1:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant 16	NM_001395267.1:c.101+1219… NM_001395267.1:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant 17	NM_001395268.1:c.53+26285… NM_001395268.1:c.53+26285A>T	N/A	Intron Variant
PDE1A transcript variant 1	NM_005019.7:c.101+121983A… NM_005019.7:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant 5	NM_001258314.3:c.	N/A	Genic Upstream Transcript Variant
PDE1A transcript variant 18	NM_001395269.1:c.	N/A	Genic Upstream Transcript Variant
PDE1A transcript variant X1	XM_011511323.3:c.101+1219… XM_011511323.3:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant X3	XM_011511324.4:c.101+1219… XM_011511324.4:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant X5	XM_011511325.4:c.53+26285… XM_011511325.4:c.53+26285A>T	N/A	Intron Variant
PDE1A transcript variant X2	XM_017004294.3:c.101+1219… XM_017004294.3:c.101+121983A>T	N/A	Intron Variant
PDE1A transcript variant X4	XM_047444688.1:c.185+1219… XM_047444688.1:c.185+121983A>T	N/A	Intron Variant
PDE1A transcript variant X6	XM_011511326.3:c.	N/A	Genic Upstream Transcript Variant
PDE1A transcript variant X7	XR_007076388.1:n.	N/A	Intron 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	T=	A
GRCh38.p14 chr 2	NC_000002.12:g.182400293=	NC_000002.12:g.182400293T>A
GRCh37.p13 chr 2	NC_000002.11:g.183265020=	NC_000002.11:g.183265020T>A
PDE1A transcript variant 2	NM_001003683.2:c.101+121983=	NM_001003683.2:c.101+121983A>T
PDE1A transcript variant 2	NM_001003683.3:c.101+121983=	NM_001003683.3:c.101+121983A>T
PDE1A transcript variant 3	NM_001258312.1:c.113+121983=	NM_001258312.1:c.113+121983A>T
PDE1A transcript variant 3	NM_001258312.3:c.113+121983=	NM_001258312.3:c.113+121983A>T
PDE1A transcript variant 4	NM_001258313.1:c.53+26285=	NM_001258313.1:c.53+26285A>T
PDE1A transcript variant 4	NM_001258313.3:c.53+26285=	NM_001258313.3:c.53+26285A>T
PDE1A transcript variant 6	NM_001363871.4:c.53+26285=	NM_001363871.4:c.53+26285A>T
PDE1A transcript variant 7	NM_001395258.2:c.101+121983=	NM_001395258.2:c.101+121983A>T
PDE1A transcript variant 8	NM_001395259.2:c.101+121983=	NM_001395259.2:c.101+121983A>T
PDE1A transcript variant 9	NM_001395260.2:c.101+121983=	NM_001395260.2:c.101+121983A>T
PDE1A transcript variant 10	NM_001395261.2:c.101+121983=	NM_001395261.2:c.101+121983A>T
PDE1A transcript variant 11	NM_001395262.1:c.101+121983=	NM_001395262.1:c.101+121983A>T
PDE1A transcript variant 12	NM_001395263.1:c.101+121983=	NM_001395263.1:c.101+121983A>T
PDE1A transcript variant 13	NM_001395264.1:c.53+26285=	NM_001395264.1:c.53+26285A>T
PDE1A transcript variant 14	NM_001395265.2:c.-212+63305=	NM_001395265.2:c.-212+63305A>T
PDE1A transcript variant 15	NM_001395266.1:c.101+121983=	NM_001395266.1:c.101+121983A>T
PDE1A transcript variant 16	NM_001395267.1:c.101+121983=	NM_001395267.1:c.101+121983A>T
PDE1A transcript variant 17	NM_001395268.1:c.53+26285=	NM_001395268.1:c.53+26285A>T
PDE1A transcript variant 1	NM_005019.4:c.101+121983=	NM_005019.4:c.101+121983A>T
PDE1A transcript variant 1	NM_005019.7:c.101+121983=	NM_005019.7:c.101+121983A>T
PDE1A transcript variant X1	XM_005246635.1:c.101+121983=	XM_005246635.1:c.101+121983A>T
PDE1A transcript variant X2	XM_005246636.1:c.53+26285=	XM_005246636.1:c.53+26285A>T
PDE1A transcript variant X1	XM_011511323.3:c.101+121983=	XM_011511323.3:c.101+121983A>T
PDE1A transcript variant X3	XM_011511324.4:c.101+121983=	XM_011511324.4:c.101+121983A>T
PDE1A transcript variant X5	XM_011511325.4:c.53+26285=	XM_011511325.4:c.53+26285A>T
PDE1A transcript variant X2	XM_017004294.3:c.101+121983=	XM_017004294.3:c.101+121983A>T
PDE1A transcript variant X4	XM_047444688.1:c.185+121983=	XM_047444688.1:c.185+121983A>T

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#.

28 SubSNP, 13 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss455670237	Sep 17, 2011 (135)
2	EVA-GONL	ss977725217	Aug 21, 2014 (142)
3	JMKIDD_LAB	ss1069764740	Aug 21, 2014 (142)
4	1000GENOMES	ss1300724262	Aug 21, 2014 (142)
5	EVA_GENOME_DK	ss1579231332	Apr 01, 2015 (144)
6	EVA_DECODE	ss1587167182	Apr 01, 2015 (144)
7	EVA_UK10K_ALSPAC	ss1605308910	Apr 01, 2015 (144)
8	EVA_UK10K_TWINSUK	ss1648302943	Apr 01, 2015 (144)
9	JJLAB	ss2021025878	Sep 14, 2016 (149)
10	HUMAN_LONGEVITY	ss2237196645	Dec 20, 2016 (150)
11	GNOMAD	ss2783663750	Nov 08, 2017 (151)
12	SWEGEN	ss2990988639	Nov 08, 2017 (151)
13	CSHL	ss3344641197	Nov 08, 2017 (151)
14	EGCUT_WGS	ss3658865450	Jul 13, 2019 (153)
15	EVA_DECODE	ss3705572126	Jul 13, 2019 (153)
16	ACPOP	ss3729174607	Jul 13, 2019 (153)
17	EVA	ss3757812180	Jul 13, 2019 (153)
18	SGDP_PRJ	ss3854128717	Apr 25, 2020 (154)
19	TOPMED	ss4536354998	Apr 26, 2021 (155)
20	1000G_HIGH_COVERAGE	ss5251226196	Oct 13, 2022 (156)
21	EVA	ss5334569727	Oct 13, 2022 (156)
22	HUGCELL_USP	ss5450924619	Oct 13, 2022 (156)
23	1000G_HIGH_COVERAGE	ss5528144029	Oct 13, 2022 (156)
24	SANFORD_IMAGENETICS	ss5630501995	Oct 13, 2022 (156)
25	TOMMO_GENOMICS	ss5686033030	Oct 13, 2022 (156)
26	EVA	ss5821282061	Oct 13, 2022 (156)
27	EVA	ss5933780537	Oct 13, 2022 (156)
28	EVA	ss5956737712	Oct 13, 2022 (156)
29	1000Genomes	NC_000002.11 - 183265020	Oct 11, 2018 (152)
30	1000Genomes_30x	NC_000002.12 - 182400293	Oct 13, 2022 (156)
31	The Avon Longitudinal Study of Parents and Children	NC_000002.11 - 183265020	Oct 11, 2018 (152)
32	Genetic variation in the Estonian population	NC_000002.11 - 183265020	Oct 11, 2018 (152)
33	The Danish reference pan genome	NC_000002.11 - 183265020	Apr 25, 2020 (154)
34	gnomAD - Genomes	NC_000002.12 - 182400293	Apr 26, 2021 (155)
35	Genome of the Netherlands Release 5	NC_000002.11 - 183265020	Apr 25, 2020 (154)
36	Northern Sweden	NC_000002.11 - 183265020	Jul 13, 2019 (153)
37	SGDP_PRJ	NC_000002.11 - 183265020	Apr 25, 2020 (154)
38	14KJPN	NC_000002.12 - 182400293	Oct 13, 2022 (156)
39	TopMed	NC_000002.12 - 182400293	Apr 26, 2021 (155)
40	UK 10K study - Twins	NC_000002.11 - 183265020	Oct 11, 2018 (152)
41	ALFA	NC_000002.12 - 182400293	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
ss1587167182	NC_000002.10:182973264:T:A	NC_000002.12:182400292:T:A	(self)
11793470, 6516553, 4603698, 5396271, 2863613, 2459472, 6145697, 6516553, ss455670237, ss977725217, ss1069764740, ss1300724262, ss1579231332, ss1605308910, ss1648302943, ss2021025878, ss2783663750, ss2990988639, ss3344641197, ss3658865450, ss3729174607, ss3757812180, ss3854128717, ss5334569727, ss5630501995, ss5821282061, ss5956737712	NC_000002.11:183265019:T:A	NC_000002.12:182400292:T:A	(self)
15669964, 84039838, 19870134, 340177877, 9928227945, ss2237196645, ss3705572126, ss4536354998, ss5251226196, ss5450924619, ss5528144029, ss5686033030, ss5933780537	NC_000002.12:182400292:T:A	NC_000002.12:182400292:T:A	(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 rs192436108

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

rs192436108