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dbSNP Short Genetic Variations

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.

rs201186828

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:930165 (GRCh38.p13) 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
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000378 (100/264690, TOPMED)
A=0.000797 (128/160658, GnomAD_exome)
A=0.000321 (45/140148, GnomAD) (+ 9 more)
A=0.00008 (6/75356, ALFA)
A=0.00102 (18/17680, ExAC)
A=0.02041 (342/16756, 8.3KJPN)
A=0.0028 (14/5008, 1000G)
A=0.0002 (1/4480, Estonian)
A=0.0110 (32/2922, KOREAN)
A=0.009 (7/790, PRJEB37584)
A=0.007 (4/600, NorthernSweden)
A=0.3 (2/6, SGDP_PRJ)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SAMD11 : Missense Variant
Publications
0 citations
Genomic View
See rs on genome
Help

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.p13 chr 1 NC_000001.11:g.930165G>A
GRCh38.p13 chr 1 NC_000001.11:g.930165G>T
GRCh37.p13 chr 1 NC_000001.10:g.865545G>A
GRCh37.p13 chr 1 NC_000001.10:g.865545G>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.83G>A R [CGG] > Q [CAG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Arg28Gln R (Arg) > Q (Gln) Missense Variant
SAMD11 transcript variant 3 NM_152486.4:c.83G>T R [CGG] > L [CTG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Arg28Leu R (Arg) > L (Leu) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.620G>A R [CGG] > Q [CAG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Arg207Gln R (Arg) > Q (Gln) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.620G>T R [CGG] > L [CTG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Arg207Leu R (Arg) > L (Leu) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.620G>A R [CGG] > Q [CAG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Arg207Gln R (Arg) > Q (Gln) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.620G>T R [CGG] > L [CTG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Arg207Leu R (Arg) > L (Leu) Missense Variant
Help

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

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 75356 G=0.99992 A=0.00008
European Sub 63916 G=0.99994 A=0.00006
African Sub 3094 G=0.9997 A=0.0003
African Others Sub 116 G=1.000 A=0.000
African American Sub 2978 G=0.9997 A=0.0003
Asian Sub 138 G=0.993 A=0.007
East Asian Sub 86 G=0.99 A=0.01
Other Asian Sub 52 G=1.00 A=0.00
Latin American 1 Sub 500 G=1.000 A=0.000
Latin American 2 Sub 648 G=1.000 A=0.000
South Asian Sub 98 G=1.00 A=0.00
Other Sub 6962 G=1.0000 A=0.0000


Help

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 G=0.999622 A=0.000378
gnomAD - Exomes Global Study-wide 160658 G=0.999203 A=0.000797
gnomAD - Exomes European Sub 78164 G=0.99971 A=0.00029
gnomAD - Exomes Asian Sub 35562 G=0.99708 A=0.00292
gnomAD - Exomes American Sub 25288 G=1.00000 A=0.00000
gnomAD - Exomes African Sub 8592 G=1.0000 A=0.0000
gnomAD - Exomes Ashkenazi Jewish Sub 8534 G=1.0000 A=0.0000
gnomAD - Exomes Other Sub 4518 G=0.9998 A=0.0002
gnomAD - Genomes Global Study-wide 140148 G=0.999679 A=0.000321
gnomAD - Genomes European Sub 75916 G=0.99980 A=0.00020
gnomAD - Genomes African Sub 41988 G=0.99998 A=0.00002
gnomAD - Genomes American Sub 13656 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3116 G=0.9913 A=0.0087
gnomAD - Genomes Other Sub 2148 G=0.9991 A=0.0009
ExAC Global Study-wide 17680 G=0.99898 A=0.00102
ExAC Asian Sub 8402 G=0.9982 A=0.0018
ExAC Europe Sub 6784 G=0.9996 A=0.0004
ExAC African Sub 1800 G=1.0000 A=0.0000
ExAC American Sub 502 G=1.000 A=0.000
ExAC Other Sub 192 G=1.000 A=0.000
8.3KJPN JAPANESE Study-wide 16756 G=0.97959 A=0.02041
1000Genomes Global Study-wide 5008 G=0.9972 A=0.0028
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=0.9871 A=0.0129
1000Genomes Europe Sub 1006 G=0.9990 A=0.0010
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9998 A=0.0002
KOREAN population from KRGDB KOREAN Study-wide 2922 G=0.9890 A=0.0110
CNV burdens in cranial meningiomas Global Study-wide 790 G=0.991 A=0.009
CNV burdens in cranial meningiomas CRM Sub 790 G=0.991 A=0.009
Northern Sweden ACPOP Study-wide 600 G=0.993 A=0.007
SGDP_PRJ Global Study-wide 6 G=0.5 A=0.3, T=0.2
Help

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 G= A T
GRCh38.p13 chr 1 NC_000001.11:g.930165= NC_000001.11:g.930165G>A NC_000001.11:g.930165G>T
GRCh37.p13 chr 1 NC_000001.10:g.865545= NC_000001.10:g.865545G>A NC_000001.10:g.865545G>T
SAMD11 transcript variant 3 NM_152486.4:c.83= NM_152486.4:c.83G>A NM_152486.4:c.83G>T
SAMD11 transcript NM_152486.3:c.83= NM_152486.3:c.83G>A NM_152486.3:c.83G>T
SAMD11 transcript NM_152486.2:c.83= NM_152486.2:c.83G>A NM_152486.2:c.83G>T
SAMD11 transcript variant 2 NM_001385640.1:c.620= NM_001385640.1:c.620G>A NM_001385640.1:c.620G>T
SAMD11 transcript variant 1 NM_001385641.1:c.620= NM_001385641.1:c.620G>A NM_001385641.1:c.620G>T
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Arg28= NP_689699.3:p.Arg28Gln NP_689699.3:p.Arg28Leu
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Arg207= NP_001372569.1:p.Arg207Gln NP_001372569.1:p.Arg207Leu
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Arg207= NP_001372570.1:p.Arg207Gln NP_001372570.1:p.Arg207Leu
sterile alpha motif domain-containing protein 11 NP_689699.2:p.Arg28= NP_689699.2:p.Arg28Gln NP_689699.2:p.Arg28Leu
Help

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#.

35 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss487561401 May 04, 2012 (137)
2 EXOME_CHIP ss491283783 May 04, 2012 (137)
3 ILLUMINA ss783457294 Sep 08, 2015 (146)
4 1000GENOMES ss1289342534 Aug 21, 2014 (142)
5 EVA_EXAC ss1685217276 Apr 01, 2015 (144)
6 ILLUMINA ss1751936466 Sep 08, 2015 (146)
7 ILLUMINA ss1917720776 Feb 12, 2016 (147)
8 ILLUMINA ss1945981595 Feb 12, 2016 (147)
9 ILLUMINA ss1958230143 Feb 12, 2016 (147)
10 HUMAN_LONGEVITY ss2159370725 Dec 20, 2016 (150)
11 TOPMED ss2321509474 Dec 20, 2016 (150)
12 GNOMAD ss2730986873 Nov 08, 2017 (151)
13 GNOMAD ss2746169440 Nov 08, 2017 (151)
14 GNOMAD ss2750649370 Nov 08, 2017 (151)
15 SWEGEN ss2986151090 Nov 08, 2017 (151)
16 ILLUMINA ss3021043165 Nov 08, 2017 (151)
17 TOPMED ss3066421290 Nov 08, 2017 (151)
18 ILLUMINA ss3634301823 Oct 11, 2018 (152)
19 ILLUMINA ss3640009189 Oct 11, 2018 (152)
20 ILLUMINA ss3644477466 Oct 11, 2018 (152)
21 ILLUMINA ss3651365217 Oct 11, 2018 (152)
22 EGCUT_WGS ss3654262363 Jul 12, 2019 (153)
23 EVA_DECODE ss3685993693 Jul 12, 2019 (153)
24 ACPOP ss3726717051 Jul 12, 2019 (153)
25 ILLUMINA ss3744337202 Jul 12, 2019 (153)
26 ILLUMINA ss3744602755 Jul 12, 2019 (153)
27 EVA ss3745721932 Jul 12, 2019 (153)
28 ILLUMINA ss3772104520 Jul 12, 2019 (153)
29 KHV_HUMAN_GENOMES ss3798744619 Jul 12, 2019 (153)
30 SGDP_PRJ ss3847998168 Apr 25, 2020 (154)
31 KRGDB ss3892840176 Apr 25, 2020 (154)
32 EVA ss3984450711 Apr 25, 2021 (155)
33 TOPMED ss4436458112 Apr 25, 2021 (155)
34 TOMMO_GENOMICS ss5142056942 Apr 25, 2021 (155)
35 EVA ss5236862237 Apr 25, 2021 (155)
36 1000Genomes NC_000001.10 - 865545 Oct 11, 2018 (152)
37 Genetic variation in the Estonian population NC_000001.10 - 865545 Oct 11, 2018 (152)
38 ExAC NC_000001.10 - 865545 Oct 11, 2018 (152)
39 gnomAD - Genomes NC_000001.11 - 930165 Apr 25, 2021 (155)
40 gnomAD - Exomes NC_000001.10 - 865545 Jul 12, 2019 (153)
41 KOREAN population from KRGDB NC_000001.10 - 865545 Apr 25, 2020 (154)
42 Northern Sweden NC_000001.10 - 865545 Jul 12, 2019 (153)
43 CNV burdens in cranial meningiomas NC_000001.10 - 865545 Apr 25, 2021 (155)
44 SGDP_PRJ NC_000001.10 - 865545 Apr 25, 2020 (154)
45 8.3KJPN NC_000001.10 - 865545 Apr 25, 2021 (155)
46 TopMed NC_000001.11 - 930165 Apr 25, 2021 (155)
47 ALFA NC_000001.11 - 930165 Apr 25, 2021 (155)
Help

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
7393, 611, 4390375, 1207, 17570, 1916, 10, 15148, 26249, ss487561401, ss491283783, ss783457294, ss1289342534, ss1685217276, ss1751936466, ss1917720776, ss1945981595, ss1958230143, ss2321509474, ss2730986873, ss2746169440, ss2750649370, ss2986151090, ss3021043165, ss3634301823, ss3640009189, ss3644477466, ss3651365217, ss3654262363, ss3726717051, ss3744337202, ss3744602755, ss3745721932, ss3772104520, ss3847998168, ss3892840176, ss3984450711, ss5142056942 NC_000001.10:865544:G:A NC_000001.11:930164:G:A (self)
87199, 32418, 64447, 9040942715, ss2159370725, ss3066421290, ss3685993693, ss3798744619, ss4436458112, ss5236862237 NC_000001.11:930164:G:A NC_000001.11:930164:G:A (self)
15148, ss3847998168 NC_000001.10:865544:G:T NC_000001.11:930164:G:T (self)
Help

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs201186828

Help

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.

Software version is: 2.0.1.post596+ae089ad