Name: rs813979
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.

rs813979

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:139959168 (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 / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: C=0.370516 (98072/264690, TOPMED)
C=0.380981 (53335/139994, GnomAD)
C=0.27047 (7643/28258, 14KJPN) (+ 21 more)
C=0.36020 (9598/26646, ALFA)
C=0.27023 (4529/16760, 8.3KJPN)
C=0.3727 (2387/6404, 1000G_30x)
C=0.3686 (1846/5008, 1000G)
C=0.3308 (1482/4480, Estonian)
C=0.3321 (1280/3854, ALSPAC)
C=0.3212 (1191/3708, TWINSUK)
C=0.2663 (778/2922, KOREAN)
C=0.3827 (724/1892, HapMap)
C=0.2757 (505/1832, Korea1K)
C=0.3097 (350/1130, Daghestan)
C=0.341 (340/998, GoNL)
C=0.160 (100/626, Chileans)
C=0.385 (231/600, NorthernSweden)
T=0.418 (117/280, SGDP_PRJ)
C=0.236 (51/216, Qatari)
C=0.299 (64/214, Vietnamese)
C=0.30 (12/40, GENOME_DK)
C=0.21 (6/28, Ancient Sardinia)
T=0.50 (11/22, Siberian)
C=0.50 (11/22, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: MAML3 : 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	26646	T=0.63980	C=0.36020
European	Sub	15670	T=0.67875	C=0.32125
African	Sub	6248	T=0.4486	C=0.5514
African Others	Sub	210	T=0.424	C=0.576
African American	Sub	6038	T=0.4495	C=0.5505
Asian	Sub	160	T=0.688	C=0.312
East Asian	Sub	102	T=0.735	C=0.265
Other Asian	Sub	58	T=0.60	C=0.40
Latin American 1	Sub	292	T=0.702	C=0.298
Latin American 2	Sub	2768	T=0.8111	C=0.1889
South Asian	Sub	110	T=0.791	C=0.209
Other	Sub	1398	T=0.6881	C=0.3119

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=0.629484	C=0.370516
gnomAD - Genomes	Global	Study-wide	139994	T=0.619019	C=0.380981
gnomAD - Genomes	European	Sub	75852	T=0.67322	C=0.32678
gnomAD - Genomes	African	Sub	41900	T=0.45232	C=0.54768
gnomAD - Genomes	American	Sub	13644	T=0.78210	C=0.21790
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	T=0.7034	C=0.2966
gnomAD - Genomes	East Asian	Sub	3128	T=0.7187	C=0.2813
gnomAD - Genomes	Other	Sub	2152	T=0.6454	C=0.3546
14KJPN	JAPANESE	Study-wide	28258	T=0.72953	C=0.27047
Allele Frequency Aggregator	Total	Global	26646	T=0.63980	C=0.36020
Allele Frequency Aggregator	European	Sub	15670	T=0.67875	C=0.32125
Allele Frequency Aggregator	African	Sub	6248	T=0.4486	C=0.5514
Allele Frequency Aggregator	Latin American 2	Sub	2768	T=0.8111	C=0.1889
Allele Frequency Aggregator	Other	Sub	1398	T=0.6881	C=0.3119
Allele Frequency Aggregator	Latin American 1	Sub	292	T=0.702	C=0.298
Allele Frequency Aggregator	Asian	Sub	160	T=0.688	C=0.312
Allele Frequency Aggregator	South Asian	Sub	110	T=0.791	C=0.209
8.3KJPN	JAPANESE	Study-wide	16760	T=0.72977	C=0.27023
1000Genomes_30x	Global	Study-wide	6404	T=0.6273	C=0.3727
1000Genomes_30x	African	Sub	1786	T=0.3953	C=0.6047
1000Genomes_30x	Europe	Sub	1266	T=0.6888	C=0.3112
1000Genomes_30x	South Asian	Sub	1202	T=0.6897	C=0.3103
1000Genomes_30x	East Asian	Sub	1170	T=0.6923	C=0.3077
1000Genomes_30x	American	Sub	980	T=0.816	C=0.184
1000Genomes	Global	Study-wide	5008	T=0.6314	C=0.3686
1000Genomes	African	Sub	1322	T=0.4077	C=0.5923
1000Genomes	East Asian	Sub	1008	T=0.6895	C=0.3105
1000Genomes	Europe	Sub	1006	T=0.6928	C=0.3072
1000Genomes	South Asian	Sub	978	T=0.679	C=0.321
1000Genomes	American	Sub	694	T=0.817	C=0.183
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.6692	C=0.3308
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.6679	C=0.3321
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.6788	C=0.3212
KOREAN population from KRGDB	KOREAN	Study-wide	2922	T=0.7337	A=0.0000, C=0.2663
HapMap	Global	Study-wide	1892	T=0.6173	C=0.3827
HapMap	American	Sub	770	T=0.706	C=0.294
HapMap	African	Sub	692	T=0.483	C=0.517
HapMap	Asian	Sub	254	T=0.681	C=0.319
HapMap	Europe	Sub	176	T=0.665	C=0.335
Korean Genome Project	KOREAN	Study-wide	1832	T=0.7243	C=0.2757
Genome-wide autozygosity in Daghestan	Global	Study-wide	1130	T=0.6903	C=0.3097
Genome-wide autozygosity in Daghestan	Daghestan	Sub	624	T=0.659	C=0.341
Genome-wide autozygosity in Daghestan	Near_East	Sub	142	T=0.754	C=0.246
Genome-wide autozygosity in Daghestan	Central Asia	Sub	122	T=0.811	C=0.189
Genome-wide autozygosity in Daghestan	Europe	Sub	108	T=0.639	C=0.361
Genome-wide autozygosity in Daghestan	South Asian	Sub	98	T=0.64	C=0.36
Genome-wide autozygosity in Daghestan	Caucasus	Sub	36	T=0.86	C=0.14
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.659	C=0.341
Chileans	Chilean	Study-wide	626	T=0.840	C=0.160
Northern Sweden	ACPOP	Study-wide	600	T=0.615	C=0.385
SGDP_PRJ	Global	Study-wide	280	T=0.418	C=0.582
Qatari	Global	Study-wide	216	T=0.764	C=0.236
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.701	C=0.299
The Danish reference pan genome	Danish	Study-wide	40	T=0.70	C=0.30
Ancient Sardinia genome-wide 1240k capture data generation and analysis	Global	Study-wide	28	T=0.79	C=0.21
Siberian	Global	Study-wide	22	T=0.50	C=0.50

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 4	NC_000004.12:g.139959168T>A
GRCh38.p14 chr 4	NC_000004.12:g.139959168T>C
GRCh37.p13 chr 4	NC_000004.11:g.140880322T>A
GRCh37.p13 chr 4	NC_000004.11:g.140880322T>C

Gene: MAML3, mastermind like transcriptional coactivator 3 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
MAML3 transcript	NM_018717.5:c.469-68201A>T	N/A	Intron Variant
MAML3 transcript variant X1	XM_047415929.1:c.469-6820… XM_047415929.1:c.469-68201A>T	N/A	Intron Variant
MAML3 transcript variant X2	XM_047415930.1:c.469-6820… XM_047415930.1:c.469-68201A>T	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	C
GRCh38.p14 chr 4	NC_000004.12:g.139959168=	NC_000004.12:g.139959168T>A	NC_000004.12:g.139959168T>C
GRCh37.p13 chr 4	NC_000004.11:g.140880322=	NC_000004.11:g.140880322T>A	NC_000004.11:g.140880322T>C
MAML3 transcript	NM_018717.4:c.469-68201=	NM_018717.4:c.469-68201A>T	NM_018717.4:c.469-68201A>G
MAML3 transcript	NM_018717.5:c.469-68201=	NM_018717.5:c.469-68201A>T	NM_018717.5:c.469-68201A>G
MAML3 transcript variant X1	XM_047415929.1:c.469-68201=	XM_047415929.1:c.469-68201A>T	XM_047415929.1:c.469-68201A>G
MAML3 transcript variant X2	XM_047415930.1:c.469-68201=	XM_047415930.1:c.469-68201A>T	XM_047415930.1:c.469-68201A>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#.

75 SubSNP, 23 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	KWOK	ss1067832	Oct 05, 2000 (86)
2	KWOK	ss1661415	Oct 18, 2000 (87)
3	SC_JCM	ss3664905	Sep 28, 2001 (100)
4	BCM_SSAHASNP	ss10180465	Jul 11, 2003 (116)
5	PERLEGEN	ss23419373	Sep 20, 2004 (123)
6	ABI	ss44556041	Mar 15, 2006 (126)
7	AFFY	ss76746584	Dec 08, 2007 (130)
8	HGSV	ss80745620	Dec 16, 2007 (130)
9	HGSV	ss85830100	Dec 16, 2007 (130)
10	HUMANGENOME_JCVI	ss99009502	Feb 06, 2009 (130)
11	KRIBB_YJKIM	ss104827843	Feb 06, 2009 (130)
12	1000GENOMES	ss108400277	Jan 23, 2009 (130)
13	1000GENOMES	ss110698288	Jan 25, 2009 (130)
14	ILLUMINA-UK	ss117213636	Feb 14, 2009 (130)
15	ENSEMBL	ss142767566	Dec 01, 2009 (131)
16	GMI	ss157984864	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss164540716	Jul 04, 2010 (132)
18	COMPLETE_GENOMICS	ss167226691	Jul 04, 2010 (132)
19	BUSHMAN	ss199263004	Jul 04, 2010 (132)
20	BCM-HGSC-SUB	ss206253123	Jul 04, 2010 (132)
21	1000GENOMES	ss221252232	Jul 14, 2010 (132)
22	1000GENOMES	ss232628719	Jul 14, 2010 (132)
23	1000GENOMES	ss239869499	Jul 15, 2010 (132)
24	GMI	ss277962405	May 04, 2012 (137)
25	PJP	ss293202612	May 09, 2011 (134)
26	TISHKOFF	ss557900516	Apr 25, 2013 (138)
27	SSMP	ss651718711	Apr 25, 2013 (138)
28	EVA-GONL	ss980756536	Aug 21, 2014 (142)
29	JMKIDD_LAB	ss1072017089	Aug 21, 2014 (142)
30	1000GENOMES	ss1312103241	Aug 21, 2014 (142)
31	HAMMER_LAB	ss1397390975	Sep 08, 2015 (146)
32	DDI	ss1430073506	Apr 01, 2015 (144)
33	EVA_GENOME_DK	ss1580808589	Apr 01, 2015 (144)
34	EVA_DECODE	ss1590268518	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1611323686	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1654317719	Apr 01, 2015 (144)
37	EVA_SVP	ss1712711236	Apr 01, 2015 (144)
38	HAMMER_LAB	ss1802300497	Sep 08, 2015 (146)
39	WEILL_CORNELL_DGM	ss1923997574	Feb 12, 2016 (147)
40	GENOMED	ss1969888994	Jul 19, 2016 (147)
41	JJLAB	ss2022586222	Sep 14, 2016 (149)
42	USC_VALOUEV	ss2150717831	Dec 20, 2016 (150)
43	HUMAN_LONGEVITY	ss2267740478	Dec 20, 2016 (150)
44	GRF	ss2706209002	Nov 08, 2017 (151)
45	GNOMAD	ss2816082984	Nov 08, 2017 (151)
46	SWEGEN	ss2995674702	Nov 08, 2017 (151)
47	BIOINF_KMB_FNS_UNIBA	ss3025070438	Nov 08, 2017 (151)
48	CSHL	ss3345997303	Nov 08, 2017 (151)
49	URBANLAB	ss3647866169	Oct 12, 2018 (152)
50	EGCUT_WGS	ss3663582579	Jul 13, 2019 (153)
51	EVA_DECODE	ss3713202871	Jul 13, 2019 (153)
52	ACPOP	ss3731673990	Jul 13, 2019 (153)
53	EVA	ss3762500610	Jul 13, 2019 (153)
54	KHV_HUMAN_GENOMES	ss3805660994	Jul 13, 2019 (153)
55	EVA	ss3828847529	Apr 26, 2020 (154)
56	EVA	ss3837872525	Apr 26, 2020 (154)
57	EVA	ss3843312349	Apr 26, 2020 (154)
58	SGDP_PRJ	ss3860210135	Apr 26, 2020 (154)
59	KRGDB	ss3906536412	Apr 26, 2020 (154)
60	KOGIC	ss3955257598	Apr 26, 2020 (154)
61	EVA	ss3985099194	Apr 26, 2021 (155)
62	TOPMED	ss4634504549	Apr 26, 2021 (155)
63	TOMMO_GENOMICS	ss5168332005	Apr 26, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5261274912	Oct 13, 2022 (156)
65	EVA	ss5352756601	Oct 13, 2022 (156)
66	HUGCELL_USP	ss5459807601	Oct 13, 2022 (156)
67	EVA	ss5507760158	Oct 13, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5543503622	Oct 13, 2022 (156)
69	SANFORD_IMAGENETICS	ss5636243677	Oct 13, 2022 (156)
70	TOMMO_GENOMICS	ss5703413504	Oct 13, 2022 (156)
71	YY_MCH	ss5805602184	Oct 13, 2022 (156)
72	EVA	ss5844813447	Oct 13, 2022 (156)
73	EVA	ss5854477697	Oct 13, 2022 (156)
74	EVA	ss5865792968	Oct 13, 2022 (156)
75	EVA	ss5964647401	Oct 13, 2022 (156)
76	1000Genomes	NC_000004.11 - 140880322	Oct 12, 2018 (152)
77	1000Genomes_30x	NC_000004.12 - 139959168	Oct 13, 2022 (156)
78	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 140880322	Oct 12, 2018 (152)
79	Chileans	NC_000004.11 - 140880322	Apr 26, 2020 (154)
80	Genome-wide autozygosity in Daghestan	NC_000004.10 - 141099772	Apr 26, 2020 (154)
81	Genetic variation in the Estonian population	NC_000004.11 - 140880322	Oct 12, 2018 (152)
82	The Danish reference pan genome	NC_000004.11 - 140880322	Apr 26, 2020 (154)
83	gnomAD - Genomes	NC_000004.12 - 139959168	Apr 26, 2021 (155)
84	Genome of the Netherlands Release 5	NC_000004.11 - 140880322	Apr 26, 2020 (154)
85	HapMap	NC_000004.12 - 139959168	Apr 26, 2020 (154)
86	KOREAN population from KRGDB	NC_000004.11 - 140880322	Apr 26, 2020 (154)
87	Korean Genome Project	NC_000004.12 - 139959168	Apr 26, 2020 (154)
88	Northern Sweden	NC_000004.11 - 140880322	Jul 13, 2019 (153)
89	Ancient Sardinia genome-wide 1240k capture data generation and analysis	NC_000004.11 - 140880322	Apr 26, 2021 (155)
90	Qatari	NC_000004.11 - 140880322	Apr 26, 2020 (154)
91	SGDP_PRJ	NC_000004.11 - 140880322	Apr 26, 2020 (154)
92	Siberian	NC_000004.11 - 140880322	Apr 26, 2020 (154)
93	8.3KJPN	NC_000004.11 - 140880322	Apr 26, 2021 (155)
94	14KJPN	NC_000004.12 - 139959168	Oct 13, 2022 (156)
95	TopMed	NC_000004.12 - 139959168	Apr 26, 2021 (155)
96	UK 10K study - Twins	NC_000004.11 - 140880322	Oct 12, 2018 (152)
97	A Vietnamese Genetic Variation Database	NC_000004.11 - 140880322	Jul 13, 2019 (153)
98	ALFA	NC_000004.12 - 139959168	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)
rs56491469	May 27, 2008 (130)
rs61524839	May 27, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
13713806, ss3906536412	NC_000004.11:140880321:T:A	NC_000004.12:139959167:T:A	(self)
ss80745620, ss85830100	NC_000004.9:141237926:T:C	NC_000004.12:139959167:T:C	(self)
366280, ss108400277, ss110698288, ss117213636, ss164540716, ss167226691, ss199263004, ss206253123, ss277962405, ss293202612, ss1397390975, ss1590268518, ss1712711236	NC_000004.10:141099771:T:C	NC_000004.12:139959167:T:C	(self)
23589868, 13118614, 328576, 9320827, 6973528, 5812409, 13713806, 4958855, 325121, 6039504, 12227115, 3234185, 26301312, 13118614, 2895148, ss221252232, ss232628719, ss239869499, ss557900516, ss651718711, ss980756536, ss1072017089, ss1312103241, ss1430073506, ss1580808589, ss1611323686, ss1654317719, ss1802300497, ss1923997574, ss1969888994, ss2022586222, ss2150717831, ss2706209002, ss2816082984, ss2995674702, ss3345997303, ss3663582579, ss3731673990, ss3762500610, ss3828847529, ss3837872525, ss3860210135, ss3906536412, ss3985099194, ss5168332005, ss5352756601, ss5507760158, ss5636243677, ss5844813447, ss5964647401	NC_000004.11:140880321:T:C	NC_000004.12:139959167:T:C	(self)
31029557, 167088404, 2722487, 11635599, 37250608, 471882105, 13479281394, ss2267740478, ss3025070438, ss3647866169, ss3713202871, ss3805660994, ss3843312349, ss3955257598, ss4634504549, ss5261274912, ss5459807601, ss5543503622, ss5703413504, ss5805602184, ss5854477697, ss5865792968	NC_000004.12:139959167:T:C	NC_000004.12:139959167:T:C	(self)
ss1067832, ss1661415, ss3664905, ss23419373, ss44556041, ss76746584, ss99009502, ss104827843, ss142767566, ss157984864	NT_016354.19:65428042:T:C	NC_000004.12:139959167:T:C	(self)
ss10180465	NT_016606.15:2399986:T:C	NC_000004.12:139959167: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 rs813979

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

rs813979