Name: rs4790979
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.

rs4790979

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr17:67347968 (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: C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.002418 (640/264690, TOPMED)
C=0.001468 (206/140296, GnomAD)
C=0.02459 (695/28258, 14KJPN) (+ 16 more)
C=0.00086 (16/18520, ALFA)
C=0.02673 (448/16760, 8.3KJPN)
C=0.0091 (58/6404, 1000G_30x)
C=0.0096 (48/5008, 1000G)
C=0.0002 (1/4480, Estonian)
C=0.0000 (0/3854, ALSPAC)
C=0.0000 (0/3708, TWINSUK)
C=0.0372 (109/2930, KOREAN)
C=0.0349 (64/1832, Korea1K)
C=0.000 (0/600, NorthernSweden)
C=0.013 (7/558, SGDP_PRJ)
C=0.000 (0/330, HapMap)
C=0.000 (0/216, Qatari)
C=0.037 (8/214, Vietnamese)
C=0.00 (0/56, Siberian)
C=0.00 (0/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: PSMD12 : 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	18520	C=0.00086	T=0.99914
European	Sub	14152	C=0.00014	T=0.99986
African	Sub	2898	C=0.0003	T=0.9997
African Others	Sub	114	C=0.000	T=1.000
African American	Sub	2784	C=0.0004	T=0.9996
Asian	Sub	112	C=0.089	T=0.911
East Asian	Sub	86	C=0.07	T=0.93
Other Asian	Sub	26	C=0.15	T=0.85
Latin American 1	Sub	146	C=0.000	T=1.000
Latin American 2	Sub	610	C=0.000	T=1.000
South Asian	Sub	98	C=0.00	T=1.00
Other	Sub	504	C=0.006	T=0.994

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	C=0.002418	T=0.997582
gnomAD - Genomes	Global	Study-wide	140296	C=0.001468	T=0.998532
gnomAD - Genomes	European	Sub	75976	C=0.00005	T=0.99995
gnomAD - Genomes	African	Sub	42052	C=0.00059	T=0.99941
gnomAD - Genomes	American	Sub	13656	C=0.00029	T=0.99971
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.0000	T=1.0000
gnomAD - Genomes	East Asian	Sub	3134	C=0.0530	T=0.9470
gnomAD - Genomes	Other	Sub	2154	C=0.0032	T=0.9968
14KJPN	JAPANESE	Study-wide	28258	C=0.02459	T=0.97541
Allele Frequency Aggregator	Total	Global	18520	C=0.00086	T=0.99914
Allele Frequency Aggregator	European	Sub	14152	C=0.00014	T=0.99986
Allele Frequency Aggregator	African	Sub	2898	C=0.0003	T=0.9997
Allele Frequency Aggregator	Latin American 2	Sub	610	C=0.000	T=1.000
Allele Frequency Aggregator	Other	Sub	504	C=0.006	T=0.994
Allele Frequency Aggregator	Latin American 1	Sub	146	C=0.000	T=1.000
Allele Frequency Aggregator	Asian	Sub	112	C=0.089	T=0.911
Allele Frequency Aggregator	South Asian	Sub	98	C=0.00	T=1.00
8.3KJPN	JAPANESE	Study-wide	16760	C=0.02673	T=0.97327
1000Genomes_30x	Global	Study-wide	6404	C=0.0091	T=0.9909
1000Genomes_30x	African	Sub	1786	C=0.0000	T=1.0000
1000Genomes_30x	Europe	Sub	1266	C=0.0000	T=1.0000
1000Genomes_30x	South Asian	Sub	1202	C=0.0000	T=1.0000
1000Genomes_30x	East Asian	Sub	1170	C=0.0496	T=0.9504
1000Genomes_30x	American	Sub	980	C=0.000	T=1.000
1000Genomes	Global	Study-wide	5008	C=0.0096	T=0.9904
1000Genomes	African	Sub	1322	C=0.0000	T=1.0000
1000Genomes	East Asian	Sub	1008	C=0.0476	T=0.9524
1000Genomes	Europe	Sub	1006	C=0.0000	T=1.0000
1000Genomes	South Asian	Sub	978	C=0.000	T=1.000
1000Genomes	American	Sub	694	C=0.000	T=1.000
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.0002	T=0.9998
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.0000	T=1.0000
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.0000	T=1.0000
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.0372	G=0.0000, T=0.9628
Korean Genome Project	KOREAN	Study-wide	1832	C=0.0349	T=0.9651
Northern Sweden	ACPOP	Study-wide	600	C=0.000	T=1.000
SGDP_PRJ	Global	Study-wide	558	C=0.013	T=0.987
HapMap	Global	Study-wide	330	C=0.000	T=1.000
HapMap	African	Sub	120	C=0.000	T=1.000
HapMap	American	Sub	120	C=0.000	T=1.000
HapMap	Asian	Sub	90	C=0.00	T=1.00
Qatari	Global	Study-wide	216	C=0.000	T=1.000
A Vietnamese Genetic Variation Database	Global	Study-wide	214	C=0.037	T=0.963
Siberian	Global	Study-wide	56	C=0.00	T=1.00
The Danish reference pan genome	Danish	Study-wide	40	C=0.00	T=1.00

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 17	NC_000017.11:g.67347968C>G
GRCh38.p14 chr 17	NC_000017.11:g.67347968C>T
GRCh37.p13 chr 17	NC_000017.10:g.65344084C>G
GRCh37.p13 chr 17	NC_000017.10:g.65344084C>T

Gene: PSMD12, proteasome 26S subunit, non-ATPase 12 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
PSMD12 transcript variant 3	NM_001316341.2:c.334-483G… NM_001316341.2:c.334-483G>C	N/A	Intron Variant
PSMD12 transcript variant 1	NM_002816.5:c.511-483G>C	N/A	Intron Variant
PSMD12 transcript variant 2	NM_174871.4:c.451-483G>C	N/A	Intron Variant
PSMD12 transcript variant X1	XM_047436440.1:c.511-483G… XM_047436440.1:c.511-483G>C	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	C=	G	T
GRCh38.p14 chr 17	NC_000017.11:g.67347968=	NC_000017.11:g.67347968C>G	NC_000017.11:g.67347968C>T
GRCh37.p13 chr 17	NC_000017.10:g.65344084=	NC_000017.10:g.65344084C>G	NC_000017.10:g.65344084C>T
PSMD12 transcript variant 3	NM_001316341.2:c.334-483=	NM_001316341.2:c.334-483G>C	NM_001316341.2:c.334-483G>A
PSMD12 transcript variant 1	NM_002816.3:c.511-483=	NM_002816.3:c.511-483G>C	NM_002816.3:c.511-483G>A
PSMD12 transcript variant 1	NM_002816.5:c.511-483=	NM_002816.5:c.511-483G>C	NM_002816.5:c.511-483G>A
PSMD12 transcript variant 2	NM_174871.2:c.451-483=	NM_174871.2:c.451-483G>C	NM_174871.2:c.451-483G>A
PSMD12 transcript variant 2	NM_174871.4:c.451-483=	NM_174871.4:c.451-483G>C	NM_174871.4:c.451-483G>A
PSMD12 transcript variant X1	XM_047436440.1:c.511-483=	XM_047436440.1:c.511-483G>C	XM_047436440.1:c.511-483G>A

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#.

83 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6611422	Feb 20, 2003 (111)
2	WI_SSAHASNP	ss11190648	Jul 11, 2003 (126)
3	BCM_SSAHASNP	ss14290613	Dec 05, 2003 (126)
4	SC_SNP	ss15839683	Feb 27, 2004 (126)
5	CSHL-HAPMAP	ss19369499	Feb 27, 2004 (126)
6	CSHL-HAPMAP	ss20041461	Feb 27, 2004 (126)
7	SSAHASNP	ss21372554	Apr 05, 2004 (126)
8	HGSV	ss78813301	Dec 07, 2007 (129)
9	HGSV	ss80682370	Dec 16, 2007 (130)
10	HGSV	ss84435082	Dec 16, 2007 (130)
11	HGSV	ss85993165	Dec 16, 2007 (130)
12	HGSV	ss86190585	Dec 16, 2007 (130)
13	BCMHGSC_JDW	ss90642725	Mar 24, 2008 (129)
14	HUMANGENOME_JCVI	ss96554950	Feb 06, 2009 (130)
15	KRIBB_YJKIM	ss104801953	Feb 06, 2009 (130)
16	BGI	ss106516415	Feb 06, 2009 (130)
17	1000GENOMES	ss109876760	Jan 24, 2009 (130)
18	1000GENOMES	ss113752675	Jan 25, 2009 (130)
19	ILLUMINA-UK	ss118107961	Feb 14, 2009 (130)
20	ENSEMBL	ss136524791	Dec 01, 2009 (131)
21	ENSEMBL	ss137156080	Dec 01, 2009 (131)
22	GMI	ss154561789	Dec 01, 2009 (131)
23	COMPLETE_GENOMICS	ss168421836	Jul 04, 2010 (132)
24	COMPLETE_GENOMICS	ss170054996	Jul 04, 2010 (132)
25	COMPLETE_GENOMICS	ss171653173	Jul 04, 2010 (132)
26	BUSHMAN	ss202710334	Jul 04, 2010 (132)
27	BCM-HGSC-SUB	ss207816826	Jul 04, 2010 (132)
28	1000GENOMES	ss227625917	Jul 14, 2010 (132)
29	1000GENOMES	ss237300748	Jul 15, 2010 (132)
30	1000GENOMES	ss243583405	Jul 15, 2010 (132)
31	BL	ss255749799	May 09, 2011 (134)
32	GMI	ss282820506	May 04, 2012 (137)
33	GMI	ss287205408	Apr 25, 2013 (138)
34	PJP	ss291983342	May 09, 2011 (134)
35	TISHKOFF	ss565369620	Apr 25, 2013 (138)
36	SSMP	ss661181121	Apr 25, 2013 (138)
37	JMKIDD_LAB	ss1081172255	Aug 21, 2014 (142)
38	1000GENOMES	ss1359312192	Aug 21, 2014 (142)
39	DDI	ss1428079865	Apr 01, 2015 (144)
40	EVA_GENOME_DK	ss1578220630	Apr 01, 2015 (144)
41	EVA_UK10K_ALSPAC	ss1635984608	Apr 01, 2015 (144)
42	EVA_UK10K_TWINSUK	ss1678978641	Apr 01, 2015 (144)
43	HAMMER_LAB	ss1808854098	Sep 08, 2015 (146)
44	WEILL_CORNELL_DGM	ss1936735541	Feb 12, 2016 (147)
45	GENOMED	ss1968422480	Jul 19, 2016 (147)
46	JJLAB	ss2029139907	Sep 14, 2016 (149)
47	USC_VALOUEV	ss2157622655	Dec 20, 2016 (150)
48	HUMAN_LONGEVITY	ss2218162118	Dec 20, 2016 (150)
49	SYSTEMSBIOZJU	ss2629064246	Nov 08, 2017 (151)
50	GRF	ss2702186269	Nov 08, 2017 (151)
51	GNOMAD	ss2951813139	Nov 08, 2017 (151)
52	SWEGEN	ss3015807906	Nov 08, 2017 (151)
53	BIOINF_KMB_FNS_UNIBA	ss3028392163	Nov 08, 2017 (151)
54	CSHL	ss3351813166	Nov 08, 2017 (151)
55	ILLUMINA	ss3625716991	Oct 12, 2018 (152)
56	URBANLAB	ss3650688974	Oct 12, 2018 (152)
57	EGCUT_WGS	ss3682676623	Jul 13, 2019 (153)
58	EVA_DECODE	ss3700797085	Jul 13, 2019 (153)
59	ACPOP	ss3742164930	Jul 13, 2019 (153)
60	EVA	ss3754861365	Jul 13, 2019 (153)
61	PACBIO	ss3788251246	Jul 13, 2019 (153)
62	PACBIO	ss3793199186	Jul 13, 2019 (153)
63	PACBIO	ss3798085135	Jul 13, 2019 (153)
64	KHV_HUMAN_GENOMES	ss3820127173	Jul 13, 2019 (153)
65	EVA	ss3834948063	Apr 27, 2020 (154)
66	EVA	ss3841085995	Apr 27, 2020 (154)
67	EVA	ss3846583875	Apr 27, 2020 (154)
68	SGDP_PRJ	ss3886093454	Apr 27, 2020 (154)
69	KRGDB	ss3935850036	Apr 27, 2020 (154)
70	KOGIC	ss3979177186	Apr 27, 2020 (154)
71	TOPMED	ss5041872711	Apr 26, 2021 (155)
72	TOMMO_GENOMICS	ss5223206340	Apr 26, 2021 (155)
73	1000G_HIGH_COVERAGE	ss5303726203	Oct 16, 2022 (156)
74	EVA	ss5428654474	Oct 16, 2022 (156)
75	HUGCELL_USP	ss5496709820	Oct 16, 2022 (156)
76	1000G_HIGH_COVERAGE	ss5607734290	Oct 16, 2022 (156)
77	SANFORD_IMAGENETICS	ss5660427580	Oct 16, 2022 (156)
78	TOMMO_GENOMICS	ss5779669087	Oct 16, 2022 (156)
79	YY_MCH	ss5816677662	Oct 16, 2022 (156)
80	EVA	ss5834207085	Oct 16, 2022 (156)
81	EVA	ss5851870907	Oct 16, 2022 (156)
82	EVA	ss5914593472	Oct 16, 2022 (156)
83	EVA	ss5951824108	Oct 16, 2022 (156)
84	1000Genomes	NC_000017.10 - 65344084	Oct 12, 2018 (152)
85	1000Genomes_30x	NC_000017.11 - 67347968	Oct 16, 2022 (156)
86	The Avon Longitudinal Study of Parents and Children	NC_000017.10 - 65344084	Oct 12, 2018 (152)
87	Genetic variation in the Estonian population	NC_000017.10 - 65344084	Oct 12, 2018 (152)
88	The Danish reference pan genome	NC_000017.10 - 65344084	Apr 27, 2020 (154)
89	gnomAD - Genomes	NC_000017.11 - 67347968	Apr 26, 2021 (155)
90	HapMap	NC_000017.11 - 67347968	Apr 27, 2020 (154)
91	KOREAN population from KRGDB	NC_000017.10 - 65344084	Apr 27, 2020 (154)
92	Korean Genome Project	NC_000017.11 - 67347968	Apr 27, 2020 (154)
93	Northern Sweden	NC_000017.10 - 65344084	Jul 13, 2019 (153)
94	Qatari	NC_000017.10 - 65344084	Apr 27, 2020 (154)
95	SGDP_PRJ	NC_000017.10 - 65344084	Apr 27, 2020 (154)
96	Siberian	NC_000017.10 - 65344084	Apr 27, 2020 (154)
97	8.3KJPN	NC_000017.10 - 65344084	Apr 26, 2021 (155)
98	14KJPN	NC_000017.11 - 67347968	Oct 16, 2022 (156)
99	TopMed	NC_000017.11 - 67347968	Apr 26, 2021 (155)
100	UK 10K study - Twins	NC_000017.10 - 65344084	Oct 12, 2018 (152)
101	A Vietnamese Genetic Variation Database	NC_000017.10 - 65344084	Jul 13, 2019 (153)
102	ALFA	NC_000017.11 - 67347968	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).

Associated ID	History Updated (Build)
rs7406915	Mar 10, 2006 (126)
rs61679219	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
43027430, ss3935850036	NC_000017.10:65344083:C:G	NC_000017.11:67347967:C:G	(self)
ss78813301, ss80682370, ss84435082, ss85993165, ss86190585, ss90642725, ss109876760, ss113752675, ss118107961, ss168421836, ss170054996, ss171653173, ss202710334, ss207816826, ss255749799, ss282820506, ss287205408, ss291983342	NC_000017.9:62774545:C:T	NC_000017.11:67347967:C:T	(self)
72579317, 40217336, 28414871, 4420397, 43027430, 15449795, 18777463, 38110434, 10139009, 81175647, 40217336, 8890551, ss227625917, ss237300748, ss243583405, ss565369620, ss661181121, ss1081172255, ss1359312192, ss1428079865, ss1578220630, ss1635984608, ss1678978641, ss1808854098, ss1936735541, ss1968422480, ss2029139907, ss2157622655, ss2629064246, ss2702186269, ss2951813139, ss3015807906, ss3351813166, ss3625716991, ss3682676623, ss3742164930, ss3754861365, ss3788251246, ss3793199186, ss3798085135, ss3834948063, ss3841085995, ss3886093454, ss3935850036, ss5223206340, ss5428654474, ss5660427580, ss5834207085, ss5951824108	NC_000017.10:65344083:C:T	NC_000017.11:67347967:C:T	(self)
95260225, 512208877, 1516601, 35555187, 113506191, 257418373, 15293301004, ss2218162118, ss3028392163, ss3650688974, ss3700797085, ss3820127173, ss3846583875, ss3979177186, ss5041872711, ss5303726203, ss5496709820, ss5607734290, ss5779669087, ss5816677662, ss5851870907, ss5914593472	NC_000017.11:67347967:C:T	NC_000017.11:67347967:C:T	(self)
ss11190648	NT_010783.13:20712745:C:T	NC_000017.11:67347967:C:T	(self)
ss14290613, ss15839683, ss19369499, ss20041461, ss21372554	NT_010783.14:24072824:C:T	NC_000017.11:67347967:C:T	(self)
ss6611422, ss96554950, ss104801953, ss106516415, ss136524791, ss137156080, ss154561789	NT_010783.15:30618235:C:T	NC_000017.11:67347967:C:T	(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 rs4790979

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

rs4790979