Name: rs4407380
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.

rs4407380

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:57636362 (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>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.368745 (97603/264690, TOPMED)
C=0.375989 (52661/140060, GnomAD)
C=0.49777 (14066/28258, 14KJPN) (+ 18 more)
C=0.40533 (9869/24348, ALFA)
C=0.49606 (8314/16760, 8.3KJPN)
C=0.3824 (2449/6404, 1000G_30x)
C=0.3882 (1944/5008, 1000G)
C=0.4634 (2076/4480, Estonian)
C=0.4261 (1642/3854, ALSPAC)
C=0.4318 (1601/3708, TWINSUK)
T=0.4911 (1439/2930, KOREAN)
C=0.3562 (674/1892, HapMap)
T=0.4738 (868/1832, Korea1K)
C=0.414 (413/998, GoNL)
C=0.407 (244/600, NorthernSweden)
T=0.308 (117/380, SGDP_PRJ)
T=0.500 (108/216, Qatari)
C=0.500 (108/216, Qatari)
C=0.407 (87/214, Vietnamese)
C=0.42 (17/40, GENOME_DK)
T=0.36 (13/36, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PDE12 : Intron Variant
DENND6A : 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	24348	T=0.59467	C=0.40533
European	Sub	18124	T=0.54905	C=0.45095
African	Sub	4114	T=0.8102	C=0.1898
African Others	Sub	148	T=0.872	C=0.128
African American	Sub	3966	T=0.8079	C=0.1921
Asian	Sub	124	T=0.597	C=0.403
East Asian	Sub	96	T=0.61	C=0.39
Other Asian	Sub	28	T=0.54	C=0.46
Latin American 1	Sub	168	T=0.548	C=0.452
Latin American 2	Sub	670	T=0.533	C=0.467
South Asian	Sub	98	T=0.54	C=0.46
Other	Sub	1050	T=0.5895	C=0.4105

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	T=0.631255	C=0.368745
gnomAD - Genomes	Global	Study-wide	140060	T=0.624011	C=0.375989
gnomAD - Genomes	European	Sub	75838	T=0.55020	C=0.44980
gnomAD - Genomes	African	Sub	41984	T=0.80676	C=0.19324
gnomAD - Genomes	American	Sub	13638	T=0.52984	C=0.47016
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.4422	C=0.5578
gnomAD - Genomes	East Asian	Sub	3124	T=0.5682	C=0.4318
gnomAD - Genomes	Other	Sub	2152	T=0.6185	C=0.3815
14KJPN	JAPANESE	Study-wide	28258	T=0.50223	C=0.49777
Allele Frequency Aggregator	Total	Global	24348	T=0.59467	C=0.40533
Allele Frequency Aggregator	European	Sub	18124	T=0.54905	C=0.45095
Allele Frequency Aggregator	African	Sub	4114	T=0.8102	C=0.1898
Allele Frequency Aggregator	Other	Sub	1050	T=0.5895	C=0.4105
Allele Frequency Aggregator	Latin American 2	Sub	670	T=0.533	C=0.467
Allele Frequency Aggregator	Latin American 1	Sub	168	T=0.548	C=0.452
Allele Frequency Aggregator	Asian	Sub	124	T=0.597	C=0.403
Allele Frequency Aggregator	South Asian	Sub	98	T=0.54	C=0.46
8.3KJPN	JAPANESE	Study-wide	16760	T=0.50394	C=0.49606
1000Genomes_30x	Global	Study-wide	6404	T=0.6176	C=0.3824
1000Genomes_30x	African	Sub	1786	T=0.8572	C=0.1428
1000Genomes_30x	Europe	Sub	1266	T=0.5292	C=0.4708
1000Genomes_30x	South Asian	Sub	1202	T=0.4559	C=0.5441
1000Genomes_30x	East Asian	Sub	1170	T=0.5829	C=0.4171
1000Genomes_30x	American	Sub	980	T=0.535	C=0.465
1000Genomes	Global	Study-wide	5008	T=0.6118	C=0.3882
1000Genomes	African	Sub	1322	T=0.8563	C=0.1437
1000Genomes	East Asian	Sub	1008	T=0.5724	C=0.4276
1000Genomes	Europe	Sub	1006	T=0.5278	C=0.4722
1000Genomes	South Asian	Sub	978	T=0.456	C=0.544
1000Genomes	American	Sub	694	T=0.545	C=0.455
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.5366	C=0.4634
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.5739	C=0.4261
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.5682	C=0.4318
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.4911	C=0.5089
HapMap	Global	Study-wide	1892	T=0.6438	C=0.3562
HapMap	American	Sub	770	T=0.560	C=0.440
HapMap	African	Sub	692	T=0.809	C=0.191
HapMap	Asian	Sub	254	T=0.508	C=0.492
HapMap	Europe	Sub	176	T=0.557	C=0.443
Korean Genome Project	KOREAN	Study-wide	1832	T=0.4738	C=0.5262
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.586	C=0.414
Northern Sweden	ACPOP	Study-wide	600	T=0.593	C=0.407
SGDP_PRJ	Global	Study-wide	380	T=0.308	C=0.692
Qatari	Global	Study-wide	216	T=0.500	C=0.500
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.593	C=0.407
The Danish reference pan genome	Danish	Study-wide	40	T=0.57	C=0.42
Siberian	Global	Study-wide	36	T=0.36	C=0.64

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 3	NC_000003.12:g.57636362T>C
GRCh37.p13 chr 3	NC_000003.11:g.57622089T>C

Gene: PDE12, phosphodiesterase 12 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PDE12 transcript variant 2	NM_001322176.2:c.1388-182… NM_001322176.2:c.1388-18262T>C	N/A	Intron Variant
PDE12 transcript variant 3	NM_001322177.2:c.	N/A	Genic Downstream Transcript Variant
PDE12 transcript variant 1	NM_177966.7:c.	N/A	Genic Downstream Transcript Variant

Gene: DENND6A, DENN domain containing 6A (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
DENND6A transcript	NM_152678.3:c.1133-1593A>G	N/A	Intron Variant
DENND6A transcript variant X2	XM_006713019.4:c.1130-159… XM_006713019.4:c.1130-1593A>G	N/A	Intron Variant
DENND6A transcript variant X4	XM_047447670.1:c.935-1593… XM_047447670.1:c.935-1593A>G	N/A	Intron Variant
DENND6A transcript variant X3	XR_007095649.1:n.	N/A	Intron Variant
DENND6A transcript variant X1	XR_245100.2: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=	C
GRCh38.p14 chr 3	NC_000003.12:g.57636362=	NC_000003.12:g.57636362T>C
GRCh37.p13 chr 3	NC_000003.11:g.57622089=	NC_000003.11:g.57622089T>C
PDE12 transcript variant 2	NM_001322176.2:c.1388-18262=	NM_001322176.2:c.1388-18262T>C
DENND6A transcript	NM_152678.2:c.1133-1593=	NM_152678.2:c.1133-1593A>G
DENND6A transcript	NM_152678.3:c.1133-1593=	NM_152678.3:c.1133-1593A>G
PDE12 transcript variant X1	XM_005264942.1:c.1388-18262=	XM_005264942.1:c.1388-18262T>C
DENND6A transcript variant X1	XM_005264943.1:c.1133-1593=	XM_005264943.1:c.1133-1593A>G
DENND6A transcript variant X2	XM_006713019.4:c.1130-1593=	XM_006713019.4:c.1130-1593A>G
DENND6A transcript variant X4	XM_047447670.1:c.935-1593=	XM_047447670.1:c.935-1593A>G

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#.

76 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss5893179	Feb 20, 2003 (111)
2	WI_SSAHASNP	ss11583706	Jul 11, 2003 (116)
3	SSAHASNP	ss21867487	Apr 05, 2004 (121)
4	ILLUMINA	ss75128428	Dec 06, 2007 (129)
5	HGSV	ss77248684	Dec 06, 2007 (129)
6	HUMANGENOME_JCVI	ss99094946	Feb 05, 2009 (130)
7	1000GENOMES	ss111746239	Jan 25, 2009 (130)
8	ILLUMINA-UK	ss117092554	Feb 14, 2009 (130)
9	KRIBB_YJKIM	ss119476249	Dec 01, 2009 (131)
10	ENSEMBL	ss135295847	Dec 01, 2009 (131)
11	GMI	ss155503948	Dec 01, 2009 (131)
12	COMPLETE_GENOMICS	ss166585997	Jul 04, 2010 (132)
13	ILLUMINA	ss173728519	Jul 04, 2010 (132)
14	BCM-HGSC-SUB	ss206191548	Jul 04, 2010 (132)
15	1000GENOMES	ss220151214	Jul 14, 2010 (132)
16	1000GENOMES	ss231831180	Jul 14, 2010 (132)
17	1000GENOMES	ss239243470	Jul 15, 2010 (132)
18	BL	ss253110406	May 09, 2011 (134)
19	GMI	ss277136023	May 04, 2012 (137)
20	GMI	ss284650071	Apr 25, 2013 (138)
21	PJP	ss292801499	May 09, 2011 (134)
22	ILLUMINA	ss537233924	Sep 08, 2015 (146)
23	TISHKOFF	ss556631891	Apr 25, 2013 (138)
24	SSMP	ss650311255	Apr 25, 2013 (138)
25	EVA-GONL	ss978620745	Aug 21, 2014 (142)
26	JMKIDD_LAB	ss1070429456	Aug 21, 2014 (142)
27	1000GENOMES	ss1304117839	Aug 21, 2014 (142)
28	DDI	ss1429427638	Apr 01, 2015 (144)
29	EVA_GENOME_DK	ss1579973842	Apr 01, 2015 (144)
30	EVA_DECODE	ss1588092349	Apr 01, 2015 (144)
31	EVA_UK10K_ALSPAC	ss1607130876	Apr 01, 2015 (144)
32	EVA_UK10K_TWINSUK	ss1650124909	Apr 01, 2015 (144)
33	EVA_SVP	ss1712577785	Apr 01, 2015 (144)
34	WEILL_CORNELL_DGM	ss1921859984	Feb 12, 2016 (147)
35	GENOMED	ss1969398616	Jul 19, 2016 (147)
36	JJLAB	ss2021488917	Sep 14, 2016 (149)
37	USC_VALOUEV	ss2149563708	Nov 08, 2017 (151)
38	HUMAN_LONGEVITY	ss2251821688	Dec 20, 2016 (150)
39	SYSTEMSBIOZJU	ss2625243254	Nov 08, 2017 (151)
40	GRF	ss2704939235	Nov 08, 2017 (151)
41	GNOMAD	ss2793297152	Nov 08, 2017 (151)
42	SWEGEN	ss2992361191	Nov 08, 2017 (151)
43	BIOINF_KMB_FNS_UNIBA	ss3024506570	Nov 08, 2017 (151)
44	CSHL	ss3345031128	Nov 08, 2017 (151)
45	ILLUMINA	ss3628667935	Oct 12, 2018 (152)
46	ILLUMINA	ss3638416736	Oct 12, 2018 (152)
47	ILLUMINA	ss3643373601	Oct 12, 2018 (152)
48	URBANLAB	ss3647409442	Oct 12, 2018 (152)
49	EGCUT_WGS	ss3660284550	Jul 13, 2019 (153)
50	EVA_DECODE	ss3709288970	Jul 13, 2019 (153)
51	ACPOP	ss3729910290	Jul 13, 2019 (153)
52	EVA	ss3760068225	Jul 13, 2019 (153)
53	PACBIO	ss3784322369	Jul 13, 2019 (153)
54	PACBIO	ss3789836782	Jul 13, 2019 (153)
55	PACBIO	ss3794710764	Jul 13, 2019 (153)
56	KHV_HUMAN_GENOMES	ss3803202836	Jul 13, 2019 (153)
57	EVA	ss3827823370	Apr 25, 2020 (154)
58	EVA	ss3837334426	Apr 25, 2020 (154)
59	EVA	ss3842760158	Apr 25, 2020 (154)
60	SGDP_PRJ	ss3855904234	Apr 25, 2020 (154)
61	KRGDB	ss3901768743	Apr 25, 2020 (154)
62	KOGIC	ss3951329641	Apr 25, 2020 (154)
63	EVA	ss4017082478	Apr 27, 2021 (155)
64	TOPMED	ss4565717394	Apr 27, 2021 (155)
65	TOMMO_GENOMICS	ss5159297184	Apr 27, 2021 (155)
66	1000G_HIGH_COVERAGE	ss5254188442	Oct 17, 2022 (156)
67	HUGCELL_USP	ss5453567088	Oct 17, 2022 (156)
68	EVA	ss5507002810	Oct 17, 2022 (156)
69	1000G_HIGH_COVERAGE	ss5532606724	Oct 17, 2022 (156)
70	SANFORD_IMAGENETICS	ss5632184847	Oct 17, 2022 (156)
71	TOMMO_GENOMICS	ss5691004565	Oct 17, 2022 (156)
72	YY_MCH	ss5803763133	Oct 17, 2022 (156)
73	EVA	ss5825794775	Oct 17, 2022 (156)
74	EVA	ss5853623414	Oct 17, 2022 (156)
75	EVA	ss5868951740	Oct 17, 2022 (156)
76	EVA	ss5960481150	Oct 17, 2022 (156)
77	1000Genomes	NC_000003.11 - 57622089	Oct 12, 2018 (152)
78	1000Genomes_30x	NC_000003.12 - 57636362	Oct 17, 2022 (156)
79	The Avon Longitudinal Study of Parents and Children	NC_000003.11 - 57622089	Oct 12, 2018 (152)
80	Genetic variation in the Estonian population	NC_000003.11 - 57622089	Oct 12, 2018 (152)
81	The Danish reference pan genome	NC_000003.11 - 57622089	Apr 25, 2020 (154)
82	gnomAD - Genomes	NC_000003.12 - 57636362	Apr 27, 2021 (155)
83	Genome of the Netherlands Release 5	NC_000003.11 - 57622089	Apr 25, 2020 (154)
84	HapMap	NC_000003.12 - 57636362	Apr 25, 2020 (154)
85	KOREAN population from KRGDB	NC_000003.11 - 57622089	Apr 25, 2020 (154)
86	Korean Genome Project	NC_000003.12 - 57636362	Apr 25, 2020 (154)
87	Northern Sweden	NC_000003.11 - 57622089	Jul 13, 2019 (153)
88	Qatari	NC_000003.11 - 57622089	Apr 25, 2020 (154)
89	SGDP_PRJ	NC_000003.11 - 57622089	Apr 25, 2020 (154)
90	Siberian	NC_000003.11 - 57622089	Apr 25, 2020 (154)
91	8.3KJPN	NC_000003.11 - 57622089	Apr 27, 2021 (155)
92	14KJPN	NC_000003.12 - 57636362	Oct 17, 2022 (156)
93	TopMed	NC_000003.12 - 57636362	Apr 27, 2021 (155)
94	UK 10K study - Twins	NC_000003.11 - 57622089	Oct 12, 2018 (152)
95	A Vietnamese Genetic Variation Database	NC_000003.11 - 57622089	Jul 13, 2019 (153)
96	ALFA	NC_000003.12 - 57636362	Apr 27, 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
ss77248684	NC_000003.9:57597128:T:C	NC_000003.12:57636361:T:C	(self)
ss111746239, ss117092554, ss166585997, ss206191548, ss253110406, ss277136023, ss284650071, ss292801499, ss1588092349, ss1712577785, ss3643373601	NC_000003.10:57597128:T:C	NC_000003.12:57636361:T:C	(self)
15309873, 8516974, 6022798, 6138781, 3734555, 8946137, 3195155, 3901914, 7921214, 2080062, 17266491, 8516974, 1849549, ss220151214, ss231831180, ss239243470, ss537233924, ss556631891, ss650311255, ss978620745, ss1070429456, ss1304117839, ss1429427638, ss1579973842, ss1607130876, ss1650124909, ss1921859984, ss1969398616, ss2021488917, ss2149563708, ss2625243254, ss2704939235, ss2793297152, ss2992361191, ss3345031128, ss3628667935, ss3638416736, ss3660284550, ss3729910290, ss3760068225, ss3784322369, ss3789836782, ss3794710764, ss3827823370, ss3837334426, ss3855904234, ss3901768743, ss4017082478, ss5159297184, ss5507002810, ss5632184847, ss5825794775, ss5960481150	NC_000003.11:57622088:T:C	NC_000003.12:57636361:T:C	(self)
20132659, 108689158, 2364567, 7707642, 24841669, 403094949, 10704690468, ss2251821688, ss3024506570, ss3647409442, ss3709288970, ss3803202836, ss3842760158, ss3951329641, ss4565717394, ss5254188442, ss5453567088, ss5532606724, ss5691004565, ss5803763133, ss5853623414, ss5868951740	NC_000003.12:57636361:T:C	NC_000003.12:57636361:T:C	(self)
ss11583706	NT_005999.15:6559897:T:C	NC_000003.12:57636361:T:C	(self)
ss21867487	NT_022517.16:57544436:T:C	NC_000003.12:57636361:T:C	(self)
ss5893179, ss75128428, ss99094946, ss119476249, ss135295847, ss155503948, ss173728519	NT_022517.18:57562088:T:C	NC_000003.12:57636361:T: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 rs4407380

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs4407380