Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation

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.

rs199789235

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:939317 (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
C>G / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00003 (1/35420, ALFA)
G=0.00179 (30/16760, 8.3KJPN)
G=0.0002 (1/5008, 1000G) (+ 2 more)
G=0.0021 (6/2922, KOREAN)
G=0.0022 (4/1830, Korea1K)
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.939317C>G
GRCh38.p13 chr 1 NC_000001.11:g.939317C>T
GRCh37.p13 chr 1 NC_000001.10:g.874697C>G
GRCh37.p13 chr 1 NC_000001.10:g.874697C>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.563C>G P [CCG] > R [CGG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Pro188Arg P (Pro) > R (Arg) Missense Variant
SAMD11 transcript variant 3 NM_152486.4:c.563C>T P [CCG] > L [CTG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Pro188Leu P (Pro) > L (Leu) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.1100C>G P [CCG] > R [CGG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Pro367Arg P (Pro) > R (Arg) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.1100C>T P [CCG] > L [CTG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Pro367Leu P (Pro) > L (Leu) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.1103C>G P [CCG] > R [CGG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Pro368Arg P (Pro) > R (Arg) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.1103C>T P [CCG] > L [CTG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Pro368Leu P (Pro) > 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 35420 C=0.99997 G=0.00000, T=0.00003
European Sub 26580 C=0.99996 G=0.00000, T=0.00004
African Sub 2918 C=1.0000 G=0.0000, T=0.0000
African Others Sub 114 C=1.000 G=0.000, T=0.000
African American Sub 2804 C=1.0000 G=0.0000, T=0.0000
Asian Sub 112 C=1.000 G=0.000, T=0.000
East Asian Sub 86 C=1.00 G=0.00, T=0.00
Other Asian Sub 26 C=1.00 G=0.00, T=0.00
Latin American 1 Sub 500 C=1.000 G=0.000, T=0.000
Latin American 2 Sub 628 C=1.000 G=0.000, T=0.000
South Asian Sub 98 C=1.00 G=0.00, T=0.00
Other Sub 4584 C=1.0000 G=0.0000, T=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
Allele Frequency Aggregator Total Global 35420 C=0.99997 G=0.00000, T=0.00003
Allele Frequency Aggregator European Sub 26580 C=0.99996 G=0.00000, T=0.00004
Allele Frequency Aggregator Other Sub 4584 C=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator African Sub 2918 C=1.0000 G=0.0000, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator Asian Sub 112 C=1.000 G=0.000, T=0.000
Allele Frequency Aggregator South Asian Sub 98 C=1.00 G=0.00, T=0.00
8.3KJPN JAPANESE Study-wide 16760 C=0.99821 G=0.00179
1000Genomes Global Study-wide 5008 C=0.9998 G=0.0002
1000Genomes African Sub 1322 C=1.0000 G=0.0000
1000Genomes East Asian Sub 1008 C=0.9990 G=0.0010
1000Genomes Europe Sub 1006 C=1.0000 G=0.0000
1000Genomes South Asian Sub 978 C=1.000 G=0.000
1000Genomes American Sub 694 C=1.000 G=0.000
KOREAN population from KRGDB KOREAN Study-wide 2922 C=0.9979 G=0.0021
Korean Genome Project KOREAN Study-wide 1830 C=0.9978 G=0.0022
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 C= G T
GRCh38.p13 chr 1 NC_000001.11:g.939317= NC_000001.11:g.939317C>G NC_000001.11:g.939317C>T
GRCh37.p13 chr 1 NC_000001.10:g.874697= NC_000001.10:g.874697C>G NC_000001.10:g.874697C>T
SAMD11 transcript variant 3 NM_152486.4:c.563= NM_152486.4:c.563C>G NM_152486.4:c.563C>T
SAMD11 transcript NM_152486.3:c.563= NM_152486.3:c.563C>G NM_152486.3:c.563C>T
SAMD11 transcript NM_152486.2:c.563= NM_152486.2:c.563C>G NM_152486.2:c.563C>T
SAMD11 transcript variant 2 NM_001385640.1:c.1103= NM_001385640.1:c.1103C>G NM_001385640.1:c.1103C>T
SAMD11 transcript variant 1 NM_001385641.1:c.1100= NM_001385641.1:c.1100C>G NM_001385641.1:c.1100C>T
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Pro188= NP_689699.3:p.Pro188Arg NP_689699.3:p.Pro188Leu
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Pro368= NP_001372569.1:p.Pro368Arg NP_001372569.1:p.Pro368Leu
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Pro367= NP_001372570.1:p.Pro367Arg NP_001372570.1:p.Pro367Leu
sterile alpha motif domain-containing protein 11 NP_689699.2:p.Pro188= NP_689699.2:p.Pro188Arg NP_689699.2:p.Pro188Leu
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#.

16 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss487561448 May 04, 2012 (137)
2 1000GENOMES ss1289342975 Aug 21, 2014 (142)
3 EVA_EXAC ss1685217549 Apr 01, 2015 (144)
4 EVA_EXAC ss1685217550 Apr 01, 2015 (144)
5 HUMAN_LONGEVITY ss2159371577 Dec 20, 2016 (150)
6 GNOMAD ss2730987250 Nov 08, 2017 (151)
7 GNOMAD ss2746169577 Nov 08, 2017 (151)
8 GNOMAD ss2750650553 Nov 08, 2017 (151)
9 TOPMED ss3066424156 Nov 08, 2017 (151)
10 TOPMED ss3066424157 Nov 08, 2017 (151)
11 EVA ss3745722066 Jul 12, 2019 (153)
12 KRGDB ss3892840599 Apr 25, 2020 (154)
13 KOGIC ss3943631963 Apr 25, 2020 (154)
14 TOPMED ss4436461376 Apr 25, 2021 (155)
15 TOPMED ss4436461377 Apr 25, 2021 (155)
16 TOMMO_GENOMICS ss5142057506 Apr 25, 2021 (155)
17 1000Genomes NC_000001.10 - 874697 Oct 11, 2018 (152)
18 ExAC

Submission ignored due to conflicting rows:
Row 4390662 (NC_000001.10:874696:C:C 91237/91244, NC_000001.10:874696:C:G 7/91244)
Row 4390663 (NC_000001.10:874696:C:C 91243/91244, NC_000001.10:874696:C:T 1/91244)

- Oct 11, 2018 (152)
19 ExAC

Submission ignored due to conflicting rows:
Row 4390662 (NC_000001.10:874696:C:C 91237/91244, NC_000001.10:874696:C:G 7/91244)
Row 4390663 (NC_000001.10:874696:C:C 91243/91244, NC_000001.10:874696:C:T 1/91244)

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

Submission ignored due to conflicting rows:
Row 89965 (NC_000001.11:939316:C:G 4/140128)
Row 89966 (NC_000001.11:939316:C:T 5/140128)

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

Submission ignored due to conflicting rows:
Row 89965 (NC_000001.11:939316:C:G 4/140128)
Row 89966 (NC_000001.11:939316:C:T 5/140128)

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

Submission ignored due to conflicting rows:
Row 1620 (NC_000001.10:874696:C:C 244006/244020, NC_000001.10:874696:C:G 14/244020)
Row 1621 (NC_000001.10:874696:C:C 244018/244020, NC_000001.10:874696:C:T 2/244020)

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

Submission ignored due to conflicting rows:
Row 1620 (NC_000001.10:874696:C:C 244006/244020, NC_000001.10:874696:C:G 14/244020)
Row 1621 (NC_000001.10:874696:C:C 244018/244020, NC_000001.10:874696:C:T 2/244020)

- Jul 12, 2019 (153)
24 KOREAN population from KRGDB NC_000001.10 - 874697 Apr 25, 2020 (154)
25 Korean Genome Project NC_000001.11 - 939317 Apr 25, 2020 (154)
26 8.3KJPN NC_000001.10 - 874697 Apr 25, 2021 (155)
27 TopMed

Submission ignored due to conflicting rows:
Row 67711 (NC_000001.11:939316:C:G 4/264690)
Row 67712 (NC_000001.11:939316:C:T 11/264690)

- Apr 25, 2021 (155)
28 TopMed

Submission ignored due to conflicting rows:
Row 67711 (NC_000001.11:939316:C:G 4/264690)
Row 67712 (NC_000001.11:939316:C:T 11/264690)

- Apr 25, 2021 (155)
29 ALFA NC_000001.11 - 939317 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
7854, 17993, 26813, ss487561448, ss1289342975, ss1685217550, ss2730987250, ss2746169577, ss2750650553, ss3745722066, ss3892840599, ss5142057506 NC_000001.10:874696:C:G NC_000001.11:939316:C:G (self)
9964, 34489, 1350269713, ss3066424156, ss3943631963, ss4436461376 NC_000001.11:939316:C:G NC_000001.11:939316:C:G (self)
ss1685217549, ss2730987250, ss2746169577, ss2750650553 NC_000001.10:874696:C:T NC_000001.11:939316:C:T (self)
34489, 1350269713, ss2159371577, ss3066424157, ss4436461377 NC_000001.11:939316:C:T NC_000001.11:939316:C: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 rs199789235

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