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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.

rs200099017

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:939117 (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 / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.00007 (3/44418, ALFA)
A=0.00006 (1/16760, 8.3KJPN)
C=0.0004 (2/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SAMD11 : Stop Gained
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.939117G>A
GRCh38.p13 chr 1 NC_000001.11:g.939117G>C
GRCh38.p13 chr 1 NC_000001.11:g.939117G>T
GRCh37.p13 chr 1 NC_000001.10:g.874497G>A
GRCh37.p13 chr 1 NC_000001.10:g.874497G>C
GRCh37.p13 chr 1 NC_000001.10:g.874497G>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.508G>A E [GAA] > K [AAA] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Glu170Lys E (Glu) > K (Lys) Missense Variant
SAMD11 transcript variant 3 NM_152486.4:c.508G>C E [GAA] > Q [CAA] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Glu170Gln E (Glu) > Q (Gln) Missense Variant
SAMD11 transcript variant 3 NM_152486.4:c.508G>T E [GAA] > * [TAA] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Glu170Ter E (Glu) > * (Ter) Stop Gained
SAMD11 transcript variant 1 NM_001385641.1:c.1045G>A E [GAA] > K [AAA] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Glu349Lys E (Glu) > K (Lys) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.1045G>C E [GAA] > Q [CAA] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Glu349Gln E (Glu) > Q (Gln) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.1045G>T E [GAA] > * [TAA] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Glu349Ter E (Glu) > * (Ter) Stop Gained
SAMD11 transcript variant 2 NM_001385640.1:c.1045G>A E [GAA] > K [AAA] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Glu349Lys E (Glu) > K (Lys) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.1045G>C E [GAA] > Q [CAA] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Glu349Gln E (Glu) > Q (Gln) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.1045G>T E [GAA] > * [TAA] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Glu349Ter E (Glu) > * (Ter) Stop Gained
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 44418 G=0.99993 A=0.00000, C=0.00007
European Sub 32648 G=0.99994 A=0.00000, C=0.00006
African Sub 3512 G=0.9997 A=0.0000, C=0.0003
African Others Sub 122 G=1.000 A=0.000, C=0.000
African American Sub 3390 G=0.9997 A=0.0000, C=0.0003
Asian Sub 168 G=1.000 A=0.000, C=0.000
East Asian Sub 112 G=1.000 A=0.000, C=0.000
Other Asian Sub 56 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 500 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 628 G=1.000 A=0.000, C=0.000
South Asian Sub 98 G=1.00 A=0.00, C=0.00
Other Sub 6864 G=1.0000 A=0.0000, C=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
8.3KJPN JAPANESE Study-wide 16760 G=0.99994 A=0.00006
1000Genomes Global Study-wide 5008 G=0.9996 C=0.0004
1000Genomes African Sub 1322 G=0.9985 C=0.0015
1000Genomes East Asian Sub 1008 G=1.0000 C=0.0000
1000Genomes Europe Sub 1006 G=1.0000 C=0.0000
1000Genomes South Asian Sub 978 G=1.000 C=0.000
1000Genomes American Sub 694 G=1.000 C=0.000
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 T
GRCh38.p13 chr 1 NC_000001.11:g.939117= NC_000001.11:g.939117G>A NC_000001.11:g.939117G>C NC_000001.11:g.939117G>T
GRCh37.p13 chr 1 NC_000001.10:g.874497= NC_000001.10:g.874497G>A NC_000001.10:g.874497G>C NC_000001.10:g.874497G>T
SAMD11 transcript variant 3 NM_152486.4:c.508= NM_152486.4:c.508G>A NM_152486.4:c.508G>C NM_152486.4:c.508G>T
SAMD11 transcript NM_152486.3:c.508= NM_152486.3:c.508G>A NM_152486.3:c.508G>C NM_152486.3:c.508G>T
SAMD11 transcript NM_152486.2:c.508= NM_152486.2:c.508G>A NM_152486.2:c.508G>C NM_152486.2:c.508G>T
SAMD11 transcript variant 2 NM_001385640.1:c.1045= NM_001385640.1:c.1045G>A NM_001385640.1:c.1045G>C NM_001385640.1:c.1045G>T
SAMD11 transcript variant 1 NM_001385641.1:c.1045= NM_001385641.1:c.1045G>A NM_001385641.1:c.1045G>C NM_001385641.1:c.1045G>T
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Glu170= NP_689699.3:p.Glu170Lys NP_689699.3:p.Glu170Gln NP_689699.3:p.Glu170Ter
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Glu349= NP_001372569.1:p.Glu349Lys NP_001372569.1:p.Glu349Gln NP_001372569.1:p.Glu349Ter
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Glu349= NP_001372570.1:p.Glu349Lys NP_001372570.1:p.Glu349Gln NP_001372570.1:p.Glu349Ter
sterile alpha motif domain-containing protein 11 NP_689699.2:p.Glu170= NP_689699.2:p.Glu170Lys NP_689699.2:p.Glu170Gln NP_689699.2:p.Glu170Ter
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#.

14 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss487561434 May 04, 2012 (137)
2 1000GENOMES ss1289342960 Aug 21, 2014 (142)
3 EVA_EXAC ss1685217497 Apr 01, 2015 (144)
4 EVA_EXAC ss1685217498 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2159371556 Dec 20, 2016 (150)
6 TOPMED ss2321510330 Dec 20, 2016 (150)
7 GNOMAD ss2730987187 Nov 08, 2017 (151)
8 GNOMAD ss2746169545 Nov 08, 2017 (151)
9 GNOMAD ss2750650516 Nov 08, 2017 (151)
10 TOPMED ss3066424087 Nov 08, 2017 (151)
11 TOPMED ss3066424088 Nov 08, 2017 (151)
12 TOPMED ss4436461290 Apr 25, 2021 (155)
13 TOPMED ss4436461291 Apr 25, 2021 (155)
14 TOMMO_GENOMICS ss5142057492 Apr 25, 2021 (155)
15 1000Genomes NC_000001.10 - 874497 Oct 11, 2018 (152)
16 ExAC

Submission ignored due to conflicting rows:
Row 4390609 (NC_000001.10:874496:G:G 49499/49500, NC_000001.10:874496:G:A 1/49500)
Row 4390610 (NC_000001.10:874496:G:G 49496/49500, NC_000001.10:874496:G:C 4/49500)

- Oct 11, 2018 (152)
17 ExAC

Submission ignored due to conflicting rows:
Row 4390609 (NC_000001.10:874496:G:G 49499/49500, NC_000001.10:874496:G:A 1/49500)
Row 4390610 (NC_000001.10:874496:G:G 49496/49500, NC_000001.10:874496:G:C 4/49500)

- Oct 11, 2018 (152)
18 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 89900 (NC_000001.11:939116:G:A 6/140246)
Row 89901 (NC_000001.11:939116:G:C 4/140246)

- Apr 25, 2021 (155)
19 gnomAD - Genomes

Submission ignored due to conflicting rows:
Row 89900 (NC_000001.11:939116:G:A 6/140246)
Row 89901 (NC_000001.11:939116:G:C 4/140246)

- Apr 25, 2021 (155)
20 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 1552 (NC_000001.10:874496:G:G 214857/214860, NC_000001.10:874496:G:A 3/214860)
Row 1553 (NC_000001.10:874496:G:G 214852/214860, NC_000001.10:874496:G:C 8/214860)
Row 1554 (NC_000001.10:874496:G:G 214859/214860, NC_000001.10:874496:G:T 1/214860)

- Jul 12, 2019 (153)
21 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 1552 (NC_000001.10:874496:G:G 214857/214860, NC_000001.10:874496:G:A 3/214860)
Row 1553 (NC_000001.10:874496:G:G 214852/214860, NC_000001.10:874496:G:C 8/214860)
Row 1554 (NC_000001.10:874496:G:G 214859/214860, NC_000001.10:874496:G:T 1/214860)

- Jul 12, 2019 (153)
22 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 1552 (NC_000001.10:874496:G:G 214857/214860, NC_000001.10:874496:G:A 3/214860)
Row 1553 (NC_000001.10:874496:G:G 214852/214860, NC_000001.10:874496:G:C 8/214860)
Row 1554 (NC_000001.10:874496:G:G 214859/214860, NC_000001.10:874496:G:T 1/214860)

- Jul 12, 2019 (153)
23 8.3KJPN NC_000001.10 - 874497 Apr 25, 2021 (155)
24 TopMed

Submission ignored due to conflicting rows:
Row 67625 (NC_000001.11:939116:G:A 12/264690)
Row 67626 (NC_000001.11:939116:G:C 5/264690)

- Apr 25, 2021 (155)
25 TopMed

Submission ignored due to conflicting rows:
Row 67625 (NC_000001.11:939116:G:A 12/264690)
Row 67626 (NC_000001.11:939116:G:C 5/264690)

- Apr 25, 2021 (155)
26 ALFA NC_000001.11 - 939117 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
26799, ss1685217497, ss2321510330, ss2730987187, ss2746169545, ss2750650516, ss5142057492 NC_000001.10:874496:G:A NC_000001.11:939116:G:A (self)
34432, 8481178909, ss2159371556, ss3066424087, ss4436461290 NC_000001.11:939116:G:A NC_000001.11:939116:G:A (self)
7839, ss487561434, ss1289342960, ss1685217498, ss2730987187 NC_000001.10:874496:G:C NC_000001.11:939116:G:C (self)
34432, 8481178909, ss2159371556, ss3066424088, ss4436461291 NC_000001.11:939116:G:C NC_000001.11:939116:G:C (self)
ss2730987187 NC_000001.10:874496:G:T NC_000001.11:939116: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 rs200099017

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