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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.

rs143282473

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:935779 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000472 (125/264690, TOPMED)
A=0.002470 (620/251022, GnomAD_exome)
A=0.002331 (327/140282, GnomAD) (+ 11 more)
A=0.002110 (255/120844, ExAC)
A=0.00010 (8/77746, PAGE_STUDY)
A=0.00107 (81/76000, ALFA)
A=0.00054 (7/13006, GO-ESP)
A=0.0004 (2/5008, 1000G)
A=0.0038 (17/4480, Estonian)
A=0.0005 (2/3854, ALSPAC)
A=0.0005 (2/3708, TWINSUK)
A=0.002 (2/998, GoNL)
A=0.008 (5/600, NorthernSweden)
A=0.026 (8/304, FINRISK)
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.935779G>A
GRCh38.p13 chr 1 NC_000001.11:g.935779G>C
GRCh37.p13 chr 1 NC_000001.10:g.871159G>A
GRCh37.p13 chr 1 NC_000001.10:g.871159G>C
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.313G>A G [GGC] > S [AGC] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Gly105Ser G (Gly) > S (Ser) Missense Variant
SAMD11 transcript variant 3 NM_152486.4:c.313G>C G [GGC] > R [CGC] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Gly105Arg G (Gly) > R (Arg) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.850G>A G [GGC] > S [AGC] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Gly284Ser G (Gly) > S (Ser) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.850G>C G [GGC] > R [CGC] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Gly284Arg G (Gly) > R (Arg) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.850G>A G [GGC] > S [AGC] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Gly284Ser G (Gly) > S (Ser) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.850G>C G [GGC] > R [CGC] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Gly284Arg G (Gly) > R (Arg) 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 76000 G=0.99893 A=0.00107
European Sub 63634 G=0.99879 A=0.00121
African Sub 3560 G=1.0000 A=0.0000
African Others Sub 122 G=1.000 A=0.000
African American Sub 3438 G=1.0000 A=0.0000
Asian Sub 168 G=1.000 A=0.000
East Asian Sub 112 G=1.000 A=0.000
Other Asian Sub 56 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 7392 G=0.9995 A=0.0005


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=0.999528 A=0.000472
gnomAD - Exomes Global Study-wide 251022 G=0.997530 A=0.002470
gnomAD - Exomes European Sub 135046 G=0.995490 A=0.004510
gnomAD - Exomes Asian Sub 49004 G=1.00000 A=0.00000
gnomAD - Exomes American Sub 34556 G=0.99988 A=0.00012
gnomAD - Exomes African Sub 16226 G=0.99994 A=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10064 G=1.00000 A=0.00000
gnomAD - Exomes Other Sub 6126 G=0.9990 A=0.0010
gnomAD - Genomes Global Study-wide 140282 G=0.997669 A=0.002331
gnomAD - Genomes European Sub 75954 G=0.99577 A=0.00423
gnomAD - Genomes African Sub 42056 G=0.99988 A=0.00012
gnomAD - Genomes American Sub 13662 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2152 G=0.9995 A=0.0005
ExAC Global Study-wide 120844 G=0.997890 A=0.002110
ExAC Europe Sub 72878 G=0.99657 A=0.00343
ExAC Asian Sub 25142 G=0.99996 A=0.00004
ExAC American Sub 11564 G=1.00000 A=0.00000
ExAC African Sub 10362 G=0.99990 A=0.00010
ExAC Other Sub 898 G=0.997 A=0.003
The PAGE Study Global Study-wide 77746 G=0.99990 A=0.00010
The PAGE Study AfricanAmerican Sub 31844 G=0.99984 A=0.00016
The PAGE Study Mexican Sub 10770 G=0.99991 A=0.00009
The PAGE Study Asian Sub 8254 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7872 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4464 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4216 G=0.9998 A=0.0002
The PAGE Study Dominican Sub 3812 G=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2442 G=0.9996 A=0.0004
The PAGE Study SouthAmerican Sub 1978 G=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1252 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 842 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13006 G=0.99946 A=0.00054
GO Exome Sequencing Project European American Sub 8600 G=0.9992 A=0.0008
GO Exome Sequencing Project African American Sub 4406 G=1.0000 A=0.0000
1000Genomes Global Study-wide 5008 G=0.9996 A=0.0004
1000Genomes African Sub 1322 G=1.0000 A=0.0000
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9980 A=0.0020
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=0.9962 A=0.0038
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9995 A=0.0005
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9995 A=0.0005
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.998 A=0.002
Northern Sweden ACPOP Study-wide 600 G=0.992 A=0.008
FINRISK Finnish from FINRISK project Study-wide 304 G=0.974 A=0.026
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 C
GRCh38.p13 chr 1 NC_000001.11:g.935779= NC_000001.11:g.935779G>A NC_000001.11:g.935779G>C
GRCh37.p13 chr 1 NC_000001.10:g.871159= NC_000001.10:g.871159G>A NC_000001.10:g.871159G>C
SAMD11 transcript variant 3 NM_152486.4:c.313= NM_152486.4:c.313G>A NM_152486.4:c.313G>C
SAMD11 transcript NM_152486.3:c.313= NM_152486.3:c.313G>A NM_152486.3:c.313G>C
SAMD11 transcript NM_152486.2:c.313= NM_152486.2:c.313G>A NM_152486.2:c.313G>C
SAMD11 transcript variant 2 NM_001385640.1:c.850= NM_001385640.1:c.850G>A NM_001385640.1:c.850G>C
SAMD11 transcript variant 1 NM_001385641.1:c.850= NM_001385641.1:c.850G>A NM_001385641.1:c.850G>C
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Gly105= NP_689699.3:p.Gly105Ser NP_689699.3:p.Gly105Arg
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Gly284= NP_001372569.1:p.Gly284Ser NP_001372569.1:p.Gly284Arg
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Gly284= NP_001372570.1:p.Gly284Ser NP_001372570.1:p.Gly284Arg
sterile alpha motif domain-containing protein 11 NP_689699.2:p.Gly105= NP_689699.2:p.Gly105Ser NP_689699.2:p.Gly105Arg
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#.

31 SubSNP, 14 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss341923330 May 09, 2011 (134)
2 1000GENOMES ss487561419 May 04, 2012 (137)
3 EXOME_CHIP ss491283794 May 04, 2012 (137)
4 EVA-GONL ss974770281 Aug 21, 2014 (142)
5 1000GENOMES ss1289342777 Aug 21, 2014 (142)
6 EVA_FINRISK ss1584003541 Apr 01, 2015 (144)
7 EVA_DECODE ss1584130178 Apr 01, 2015 (144)
8 EVA_UK10K_ALSPAC ss1599379517 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1642373550 Apr 01, 2015 (144)
10 EVA_EXAC ss1685217400 Apr 01, 2015 (144)
11 ILLUMINA ss1958230168 Feb 12, 2016 (147)
12 HUMAN_LONGEVITY ss2159371171 Dec 20, 2016 (150)
13 TOPMED ss2321509933 Dec 20, 2016 (150)
14 GNOMAD ss2730987059 Nov 08, 2017 (151)
15 GNOMAD ss2746169504 Nov 08, 2017 (151)
16 GNOMAD ss2750650040 Nov 08, 2017 (151)
17 SWEGEN ss2986151186 Nov 08, 2017 (151)
18 ILLUMINA ss3021043186 Nov 08, 2017 (151)
19 TOPMED ss3066422986 Nov 08, 2017 (151)
20 ILLUMINA ss3634301833 Oct 11, 2018 (152)
21 ILLUMINA ss3640009199 Oct 11, 2018 (152)
22 ILLUMINA ss3644477476 Oct 11, 2018 (152)
23 ILLUMINA ss3651365238 Oct 11, 2018 (152)
24 EGCUT_WGS ss3654262466 Jul 12, 2019 (153)
25 EVA_DECODE ss3685993825 Jul 12, 2019 (153)
26 ACPOP ss3726717107 Jul 12, 2019 (153)
27 ILLUMINA ss3744602765 Jul 12, 2019 (153)
28 PAGE_CC ss3770778571 Jul 12, 2019 (153)
29 EVA ss3823541317 Apr 25, 2020 (154)
30 VINODS ss4017889338 Apr 25, 2021 (155)
31 TOPMED ss4436459919 Apr 25, 2021 (155)
32 1000Genomes NC_000001.10 - 871159 Oct 11, 2018 (152)
33 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 871159 Oct 11, 2018 (152)
34 Genetic variation in the Estonian population NC_000001.10 - 871159 Oct 11, 2018 (152)
35 ExAC NC_000001.10 - 871159 Oct 11, 2018 (152)
36 FINRISK NC_000001.10 - 871159 Apr 25, 2020 (154)
37 gnomAD - Genomes NC_000001.11 - 935779 Apr 25, 2021 (155)
38 gnomAD - Exomes NC_000001.10 - 871159 Jul 12, 2019 (153)
39 GO Exome Sequencing Project NC_000001.10 - 871159 Oct 11, 2018 (152)
40 Genome of the Netherlands Release 5 NC_000001.10 - 871159 Apr 25, 2020 (154)
41 Northern Sweden NC_000001.10 - 871159 Jul 12, 2019 (153)
42 The PAGE Study NC_000001.11 - 935779 Jul 12, 2019 (153)
43 TopMed NC_000001.11 - 935779 Apr 25, 2021 (155)
44 UK 10K study - Twins NC_000001.10 - 871159 Oct 11, 2018 (152)
45 ALFA NC_000001.11 - 935779 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
ss1584130178 NC_000001.9:861021:G:A NC_000001.11:935778:G:A (self)
7650, 1602, 714, 4390509, 2, 1410, 54, 1147, 1972, 1602, ss341923330, ss487561419, ss491283794, ss974770281, ss1289342777, ss1584003541, ss1599379517, ss1642373550, ss1685217400, ss1958230168, ss2321509933, ss2730987059, ss2746169504, ss2750650040, ss2986151186, ss3021043186, ss3634301833, ss3640009199, ss3644477476, ss3651365238, ss3654262466, ss3726717107, ss3744602765, ss3823541317 NC_000001.10:871158:G:A NC_000001.11:935778:G:A (self)
88723, 40, 33552, 66254, 14485548703, ss2159371171, ss3066422986, ss3685993825, ss3770778571, ss4436459919 NC_000001.11:935778:G:A NC_000001.11:935778:G:A (self)
ss4017889338 NC_000001.11:935778:G:C NC_000001.11:935778:G:C
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 rs143282473

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