Name: rs139437968
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.

rs139437968

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:939382 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.000280 (74/264690, TOPMED)
T=0.000571 (142/248708, GnomAD_exome)
T=0.000314 (44/140092, GnomAD) (+ 14 more)
T=0.000637 (72/113048, ExAC)
T=0.000437 (48/109796, ALFA)
T=0.00009 (7/77768, PAGE_STUDY)
T=0.00439 (124/28258, 14KJPN)
T=0.00430 (72/16760, 8.3KJPN)
T=0.00023 (3/13002, GO-ESP)
T=0.0014 (9/6404, 1000G_30x)
T=0.0016 (8/5008, 1000G)
T=0.0036 (16/4480, Estonian)
T=0.0058 (17/2922, KOREAN)
T=0.0093 (17/1832, Korea1K)
T=0.013 (10/790, PRJEB37584)
C=0.5 (2/4, SGDP_PRJ)
T=0.5 (2/4, SGDP_PRJ)

Clinical Significance: Reported in ClinVar
Gene : Consequence: SAMD11 : Missense 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	126206	C=0.999604	T=0.000396
European	Sub	101600	C=0.999587	T=0.000413
African	Sub	8992	C=0.9999	T=0.0001
African Others	Sub	308	C=1.000	T=0.000
African American	Sub	8684	C=0.9999	T=0.0001
Asian	Sub	232	C=1.000	T=0.000
East Asian	Sub	150	C=1.000	T=0.000
Other Asian	Sub	82	C=1.00	T=0.00
Latin American 1	Sub	506	C=1.000	T=0.000
Latin American 2	Sub	650	C=1.000	T=0.000
South Asian	Sub	104	C=1.000	T=0.000
Other	Sub	14122	C=0.99950	T=0.00050

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=0.999720	T=0.000280
gnomAD - Exomes	Global	Study-wide	248708	C=0.999429	T=0.000571
gnomAD - Exomes	European	Sub	133530	C=0.999760	T=0.000240
gnomAD - Exomes	Asian	Sub	48816	C=0.99830	T=0.00170
gnomAD - Exomes	American	Sub	34416	C=0.99988	T=0.00012
gnomAD - Exomes	African	Sub	15886	C=1.00000	T=0.00000
gnomAD - Exomes	Ashkenazi Jewish	Sub	9980	C=0.9981	T=0.0019
gnomAD - Exomes	Other	Sub	6080	C=0.9993	T=0.0007
gnomAD - Genomes	Global	Study-wide	140092	C=0.999686	T=0.000314
gnomAD - Genomes	European	Sub	75910	C=0.99964	T=0.00036
gnomAD - Genomes	African	Sub	41912	C=0.99998	T=0.00002
gnomAD - Genomes	American	Sub	13660	C=1.00000	T=0.00000
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	C=0.9985	T=0.0015
gnomAD - Genomes	East Asian	Sub	3132	C=0.9968	T=0.0032
gnomAD - Genomes	Other	Sub	2154	C=0.9995	T=0.0005
ExAC	Global	Study-wide	113048	C=0.999363	T=0.000637
ExAC	Europe	Sub	67878	C=0.99966	T=0.00034
ExAC	Asian	Sub	24056	C=0.99817	T=0.00183
ExAC	American	Sub	11024	C=0.99982	T=0.00018
ExAC	African	Sub	9296	C=1.0000	T=0.0000
ExAC	Other	Sub	794	C=0.996	T=0.004
Allele Frequency Aggregator	Total	Global	109796	C=0.999563	T=0.000437
Allele Frequency Aggregator	European	Sub	91462	C=0.99955	T=0.00045
Allele Frequency Aggregator	Other	Sub	12688	C=0.99953	T=0.00047
Allele Frequency Aggregator	African	Sub	4154	C=0.9998	T=0.0002
Allele Frequency Aggregator	Latin American 2	Sub	650	C=1.000	T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	506	C=1.000	T=0.000
Allele Frequency Aggregator	Asian	Sub	232	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	104	C=1.000	T=0.000
The PAGE Study	Global	Study-wide	77768	C=0.99991	T=0.00009
The PAGE Study	AfricanAmerican	Sub	31954	C=0.99994	T=0.00006
The PAGE Study	Mexican	Sub	10768	C=1.00000	T=0.00000
The PAGE Study	Asian	Sub	8136	C=0.9994	T=0.0006
The PAGE Study	PuertoRican	Sub	7880	C=1.0000	T=0.0000
The PAGE Study	NativeHawaiian	Sub	4462	C=1.0000	T=0.0000
The PAGE Study	Cuban	Sub	4224	C=1.0000	T=0.0000
The PAGE Study	Dominican	Sub	3822	C=1.0000	T=0.0000
The PAGE Study	CentralAmerican	Sub	2446	C=1.0000	T=0.0000
The PAGE Study	SouthAmerican	Sub	1980	C=1.0000	T=0.0000
The PAGE Study	NativeAmerican	Sub	1254	C=1.0000	T=0.0000
The PAGE Study	SouthAsian	Sub	842	C=1.000	T=0.000
14KJPN	JAPANESE	Study-wide	28258	C=0.99561	T=0.00439
8.3KJPN	JAPANESE	Study-wide	16760	C=0.99570	T=0.00430
GO Exome Sequencing Project	Global	Study-wide	13002	C=0.99977	T=0.00023
GO Exome Sequencing Project	European American	Sub	8600	C=0.9997	T=0.0003
GO Exome Sequencing Project	African American	Sub	4402	C=1.0000	T=0.0000
1000Genomes_30x	Global	Study-wide	6404	C=0.9986	T=0.0014
1000Genomes_30x	African	Sub	1786	C=1.0000	T=0.0000
1000Genomes_30x	Europe	Sub	1266	C=0.9992	T=0.0008
1000Genomes_30x	South Asian	Sub	1202	C=1.0000	T=0.0000
1000Genomes_30x	East Asian	Sub	1170	C=0.9932	T=0.0068
1000Genomes_30x	American	Sub	980	C=1.000	T=0.000
1000Genomes	Global	Study-wide	5008	C=0.9984	T=0.0016
1000Genomes	African	Sub	1322	C=1.0000	T=0.0000
1000Genomes	East Asian	Sub	1008	C=0.9931	T=0.0069
1000Genomes	Europe	Sub	1006	C=0.9990	T=0.0010
1000Genomes	South Asian	Sub	978	C=1.000	T=0.000
1000Genomes	American	Sub	694	C=1.000	T=0.000
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9964	T=0.0036
KOREAN population from KRGDB	KOREAN	Study-wide	2922	C=0.9942	T=0.0058
Korean Genome Project	KOREAN	Study-wide	1832	C=0.9907	T=0.0093
CNV burdens in cranial meningiomas	Global	Study-wide	790	C=0.987	T=0.013
CNV burdens in cranial meningiomas	CRM	Sub	790	C=0.987	T=0.013
SGDP_PRJ	Global	Study-wide	4	C=0.5	T=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 1	NC_000001.11:g.939382C>T
GRCh37.p13 chr 1	NC_000001.10:g.874762C>T

Gene: SAMD11, sterile alpha motif domain containing 11 (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
SAMD11 transcript variant 3	NM_152486.4:c.628C>T	R [CGC] > C [TGC]	Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3	NP_689699.3:p.Arg210Cys	R (Arg) > C (Cys)	Missense Variant
SAMD11 transcript variant 1	NM_001385641.1:c.1165C>T	R [CGC] > C [TGC]	Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1	NP_001372570.1:p.Arg389Cys	R (Arg) > C (Cys)	Missense Variant
SAMD11 transcript variant 2	NM_001385640.1:c.1168C>T	R [CGC] > C [TGC]	Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2	NP_001372569.1:p.Arg390Cys	R (Arg) > C (Cys)	Missense 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.

Allele: T (allele ID: 1067616 )

ClinVar Accession	Disease Names	Clinical Significance
RCV001393608.4	not provided	Likely-Benign

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=	T
GRCh38.p14 chr 1	NC_000001.11:g.939382=	NC_000001.11:g.939382C>T
GRCh37.p13 chr 1	NC_000001.10:g.874762=	NC_000001.10:g.874762C>T
SAMD11 transcript variant 3	NM_152486.4:c.628=	NM_152486.4:c.628C>T
SAMD11 transcript	NM_152486.3:c.628=	NM_152486.3:c.628C>T
SAMD11 transcript	NM_152486.2:c.628=	NM_152486.2:c.628C>T
SAMD11 transcript variant 2	NM_001385640.1:c.1168=	NM_001385640.1:c.1168C>T
SAMD11 transcript variant 1	NM_001385641.1:c.1165=	NM_001385641.1:c.1165C>T
sterile alpha motif domain-containing protein 11 isoform 3	NP_689699.3:p.Arg210=	NP_689699.3:p.Arg210Cys
sterile alpha motif domain-containing protein 11 isoform 2	NP_001372569.1:p.Arg390=	NP_001372569.1:p.Arg390Cys
sterile alpha motif domain-containing protein 11 isoform 1	NP_001372570.1:p.Arg389=	NP_001372570.1:p.Arg389Cys
sterile alpha motif domain-containing protein 11	NP_689699.2:p.Arg210=	NP_689699.2:p.Arg210Cys

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#.

47 SubSNP, 16 Frequency, 1 ClinVar submissions

No	Submitter	Submission ID	Date (Build)
1	1000GENOMES	ss328358694	May 09, 2011 (134)
2	1000GENOMES	ss489713603	May 04, 2012 (137)
3	EXOME_CHIP	ss491283804	May 04, 2012 (137)
4	NHLBI-ESP	ss712260263	Apr 25, 2013 (138)
5	ILLUMINA	ss783369553	Sep 08, 2015 (146)
6	JMKIDD_LAB	ss1067414245	Aug 21, 2014 (142)
7	1000GENOMES	ss1289342980	Aug 21, 2014 (142)
8	BGI	ss1558271000	Apr 01, 2015 (144)
9	EVA_EXAC	ss1685217569	Apr 01, 2015 (144)
10	ILLUMINA	ss1751936834	Sep 08, 2015 (146)
11	ILLUMINA	ss1917720793	Feb 12, 2016 (147)
12	ILLUMINA	ss1945981612	Feb 12, 2016 (147)
13	ILLUMINA	ss1958230187	Feb 12, 2016 (147)
14	HUMAN_LONGEVITY	ss2159371588	Dec 20, 2016 (150)
15	GRF	ss2697376396	Nov 08, 2017 (151)
16	GNOMAD	ss2730987272	Nov 08, 2017 (151)
17	GNOMAD	ss2746169582	Nov 08, 2017 (151)
18	GNOMAD	ss2750650558	Nov 08, 2017 (151)
19	ILLUMINA	ss3021043201	Nov 08, 2017 (151)
20	ILLUMINA	ss3634301842	Oct 11, 2018 (152)
21	ILLUMINA	ss3640009208	Oct 11, 2018 (152)
22	ILLUMINA	ss3644477484	Oct 11, 2018 (152)
23	ILLUMINA	ss3651365253	Oct 11, 2018 (152)
24	EGCUT_WGS	ss3654262536	Jul 12, 2019 (153)
25	ILLUMINA	ss3724988136	Jul 12, 2019 (153)
26	ILLUMINA	ss3744337219	Jul 12, 2019 (153)
27	ILLUMINA	ss3744602774	Jul 12, 2019 (153)
28	EVA	ss3745722070	Jul 12, 2019 (153)
29	PAGE_CC	ss3770778582	Jul 12, 2019 (153)
30	ILLUMINA	ss3772104537	Jul 12, 2019 (153)
31	KHV_HUMAN_GENOMES	ss3798744753	Jul 12, 2019 (153)
32	EVA	ss3823541356	Apr 25, 2020 (154)
33	SGDP_PRJ	ss3847998635	Apr 25, 2020 (154)
34	KRGDB	ss3892840602	Apr 25, 2020 (154)
35	KOGIC	ss3943631965	Apr 25, 2020 (154)
36	EVA	ss3984450714	Apr 25, 2021 (155)
37	TOPMED	ss4436461407	Apr 25, 2021 (155)
38	TOMMO_GENOMICS	ss5142057510	Apr 25, 2021 (155)
39	EVA	ss5236862241	Apr 25, 2021 (155)
40	1000G_HIGH_COVERAGE	ss5240866941	Oct 12, 2022 (156)
41	EVA	ss5316189079	Oct 12, 2022 (156)
42	1000G_HIGH_COVERAGE	ss5512492908	Oct 12, 2022 (156)
43	SANFORD_IMAGENETICS	ss5624751737	Oct 12, 2022 (156)
44	TOMMO_GENOMICS	ss5666198559	Oct 12, 2022 (156)
45	EVA	ss5847521237	Oct 12, 2022 (156)
46	EVA	ss5906707735	Oct 12, 2022 (156)
47	EVA	ss5936584326	Oct 12, 2022 (156)
48	1000Genomes	NC_000001.10 - 874762	Oct 11, 2018 (152)
49	1000Genomes_30x	NC_000001.11 - 939382	Oct 12, 2022 (156)
50	Genetic variation in the Estonian population	NC_000001.10 - 874762	Oct 11, 2018 (152)
51	ExAC	NC_000001.10 - 874762	Oct 11, 2018 (152)
52	gnomAD - Genomes	NC_000001.11 - 939382	Apr 25, 2021 (155)
53	gnomAD - Exomes	NC_000001.10 - 874762	Jul 12, 2019 (153)
54	GO Exome Sequencing Project	NC_000001.10 - 874762	Oct 11, 2018 (152)
55	KOREAN population from KRGDB	NC_000001.10 - 874762	Apr 25, 2020 (154)
56	Korean Genome Project	NC_000001.11 - 939382	Apr 25, 2020 (154)
57	The PAGE Study	NC_000001.11 - 939382	Jul 12, 2019 (153)
58	CNV burdens in cranial meningiomas	NC_000001.10 - 874762	Apr 25, 2021 (155)
59	SGDP_PRJ	NC_000001.10 - 874762	Apr 25, 2020 (154)
60	8.3KJPN	NC_000001.10 - 874762	Apr 25, 2021 (155)
61	14KJPN	NC_000001.11 - 939382	Oct 12, 2022 (156)
62	TopMed	NC_000001.11 - 939382	Apr 25, 2021 (155)
63	ALFA	NC_000001.11 - 939382	Apr 25, 2021 (155)
64	ClinVar	RCV001393608.4	Oct 12, 2022 (156)

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
ss1558271000	NC_000001.9:864624:C:T	NC_000001.11:939381:C:T	(self)
7859, 784, 4390682, 1648, 93, 17996, 13, 15615, 26817, ss328358694, ss489713603, ss491283804, ss712260263, ss783369553, ss1067414245, ss1289342980, ss1685217569, ss1751936834, ss1917720793, ss1945981612, ss1958230187, ss2697376396, ss2730987272, ss2746169582, ss2750650558, ss3021043201, ss3634301842, ss3640009208, ss3644477484, ss3651365253, ss3654262536, ss3744337219, ss3744602774, ss3745722070, ss3772104537, ss3823541356, ss3847998635, ss3892840602, ss3984450714, ss5142057510, ss5316189079, ss5624751737, ss5847521237, ss5936584326	NC_000001.10:874761:C:T	NC_000001.11:939381:C:T	(self)
RCV001393608.4, 18843, 89984, 9966, 51, 35663, 67742, 4497853122, ss2159371588, ss3724988136, ss3770778582, ss3798744753, ss3943631965, ss4436461407, ss5236862241, ss5240866941, ss5512492908, ss5666198559, ss5906707735	NC_000001.11:939381:C:T	NC_000001.11:939381: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 rs139437968

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

rs139437968