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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.

rs144317111

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:931049 (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=0.000151 (40/264690, TOPMED)
T=0.000104 (26/250732, GnomAD_exome)
T=0.000135 (19/140302, GnomAD) (+ 6 more)
T=0.000229 (29/126608, ALFA)
T=0.000075 (9/120220, ExAC)
T=0.00008 (6/78662, PAGE_STUDY)
T=0.00023 (3/13006, GO-ESP)
T=0.0003 (1/3854, ALSPAC)
T=0.0000 (0/3708, TWINSUK)
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 143020 C=0.999769 T=0.000231
European Sub 118262 C=0.999729 T=0.000271
African Sub 8944 C=1.0000 T=0.0000
African Others Sub 308 C=1.000 T=0.000
African American Sub 8636 C=1.0000 T=0.0000
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 14322 C=0.99993 T=0.00007


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 C=0.999849 T=0.000151
gnomAD - Exomes Global Study-wide 250732 C=0.999896 T=0.000104
gnomAD - Exomes European Sub 134824 C=0.999822 T=0.000178
gnomAD - Exomes Asian Sub 48994 C=1.00000 T=0.00000
gnomAD - Exomes American Sub 34578 C=1.00000 T=0.00000
gnomAD - Exomes African Sub 16184 C=0.99988 T=0.00012
gnomAD - Exomes Ashkenazi Jewish Sub 10042 C=1.00000 T=0.00000
gnomAD - Exomes Other Sub 6110 C=1.0000 T=0.0000
gnomAD - Genomes Global Study-wide 140302 C=0.999865 T=0.000135
gnomAD - Genomes European Sub 75964 C=0.99980 T=0.00020
gnomAD - Genomes African Sub 42060 C=0.99995 T=0.00005
gnomAD - Genomes American Sub 13666 C=0.99985 T=0.00015
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=1.0000 T=0.0000
gnomAD - Genomes East Asian Sub 3134 C=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2154 C=1.0000 T=0.0000
Allele Frequency Aggregator Total Global 126608 C=0.999771 T=0.000229
Allele Frequency Aggregator European Sub 108122 C=0.999741 T=0.000259
Allele Frequency Aggregator Other Sub 12888 C=0.99992 T=0.00008
Allele Frequency Aggregator African Sub 4106 C=1.0000 T=0.0000
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
ExAC Global Study-wide 120220 C=0.999925 T=0.000075
ExAC Europe Sub 72384 C=0.99988 T=0.00012
ExAC Asian Sub 25124 C=1.00000 T=0.00000
ExAC American Sub 11554 C=1.00000 T=0.00000
ExAC African Sub 10268 C=1.00000 T=0.00000
ExAC Other Sub 890 C=1.000 T=0.000
The PAGE Study Global Study-wide 78662 C=0.99992 T=0.00008
The PAGE Study AfricanAmerican Sub 32488 C=0.99991 T=0.00009
The PAGE Study Mexican Sub 10810 C=1.00000 T=0.00000
The PAGE Study Asian Sub 8316 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4526 C=0.9993 T=0.0007
The PAGE Study Cuban Sub 4228 C=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 C=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 C=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 C=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 C=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
GO Exome Sequencing Project Global Study-wide 13006 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 4406 C=1.0000 T=0.0000
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9997 T=0.0003
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.0000 T=0.0000
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.p14 chr 1 NC_000001.11:g.931049C>T
GRCh37.p13 chr 1 NC_000001.10:g.866429C>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.265C>T H [CAC] > Y [TAC] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.His89Tyr H (His) > Y (Tyr) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.802C>T H [CAC] > Y [TAC] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.His268Tyr H (His) > Y (Tyr) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.802C>T H [CAC] > Y [TAC] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.His268Tyr H (His) > Y (Tyr) 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.

Allele: T (allele ID: 939755 )
ClinVar Accession Disease Names Clinical Significance
RCV001213858.5 not provided Uncertain-Significance
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= T
GRCh38.p14 chr 1 NC_000001.11:g.931049= NC_000001.11:g.931049C>T
GRCh37.p13 chr 1 NC_000001.10:g.866429= NC_000001.10:g.866429C>T
SAMD11 transcript variant 3 NM_152486.4:c.265= NM_152486.4:c.265C>T
SAMD11 transcript NM_152486.3:c.265= NM_152486.3:c.265C>T
SAMD11 transcript NM_152486.2:c.265= NM_152486.2:c.265C>T
SAMD11 transcript variant 2 NM_001385640.1:c.802= NM_001385640.1:c.802C>T
SAMD11 transcript variant 1 NM_001385641.1:c.802= NM_001385641.1:c.802C>T
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.His89= NP_689699.3:p.His89Tyr
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.His268= NP_001372569.1:p.His268Tyr
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.His268= NP_001372570.1:p.His268Tyr
sterile alpha motif domain-containing protein 11 NP_689699.2:p.His89= NP_689699.2:p.His89Tyr
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#.

34 SubSNP, 9 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss341923319 May 09, 2011 (134)
2 EXOME_CHIP ss491283791 May 04, 2012 (137)
3 CLINSEQ_SNP ss491581629 May 04, 2012 (137)
4 ILLUMINA ss780856948 Sep 08, 2015 (146)
5 ILLUMINA ss783541121 Sep 08, 2015 (146)
6 EVA_UK10K_ALSPAC ss1599379438 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1642373471 Apr 01, 2015 (144)
8 EVA_EXAC ss1685217348 Apr 01, 2015 (144)
9 ILLUMINA ss1751936529 Sep 08, 2015 (146)
10 ILLUMINA ss1917720784 Feb 12, 2016 (147)
11 ILLUMINA ss1945981603 Feb 12, 2016 (147)
12 ILLUMINA ss1958230156 Feb 12, 2016 (147)
13 HUMAN_LONGEVITY ss2159370806 Dec 20, 2016 (150)
14 GNOMAD ss2730986987 Nov 08, 2017 (151)
15 GNOMAD ss2746169475 Nov 08, 2017 (151)
16 GNOMAD ss2750649467 Nov 08, 2017 (151)
17 AFFY ss2984841004 Nov 08, 2017 (151)
18 ILLUMINA ss3021043175 Nov 08, 2017 (151)
19 ILLUMINA ss3626006652 Oct 11, 2018 (152)
20 ILLUMINA ss3634301831 Oct 11, 2018 (152)
21 ILLUMINA ss3640009197 Oct 11, 2018 (152)
22 ILLUMINA ss3644477474 Oct 11, 2018 (152)
23 ILLUMINA ss3651365227 Oct 11, 2018 (152)
24 ILLUMINA ss3653614754 Oct 11, 2018 (152)
25 ILLUMINA ss3724988118 Jul 12, 2019 (153)
26 ILLUMINA ss3744337210 Jul 12, 2019 (153)
27 ILLUMINA ss3744602763 Jul 12, 2019 (153)
28 PAGE_CC ss3770778564 Jul 12, 2019 (153)
29 ILLUMINA ss3772104528 Jul 12, 2019 (153)
30 EVA ss3823541303 Apr 25, 2020 (154)
31 TOPMED ss4436458413 Apr 25, 2021 (155)
32 EVA ss5847521225 Oct 12, 2022 (156)
33 EVA ss5936584112 Oct 12, 2022 (156)
34 EVA ss5979259803 Oct 12, 2022 (156)
35 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 866429 Oct 11, 2018 (152)
36 ExAC NC_000001.10 - 866429 Oct 11, 2018 (152)
37 gnomAD - Genomes NC_000001.11 - 931049 Apr 25, 2021 (155)
38 gnomAD - Exomes NC_000001.10 - 866429 Jul 12, 2019 (153)
39 GO Exome Sequencing Project NC_000001.10 - 866429 Oct 11, 2018 (152)
40 The PAGE Study NC_000001.11 - 931049 Jul 12, 2019 (153)
41 TopMed NC_000001.11 - 931049 Apr 25, 2021 (155)
42 UK 10K study - Twins NC_000001.10 - 866429 Oct 11, 2018 (152)
43 ALFA NC_000001.11 - 931049 Apr 25, 2021 (155)
44 ClinVar RCV001213858.5 Oct 12, 2022 (156)
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
ss491581629 NC_000001.9:856291:C:T NC_000001.11:931048:C:T (self)
1516, 4390452, 1330, 40, 1516, ss341923319, ss491283791, ss780856948, ss783541121, ss1599379438, ss1642373471, ss1685217348, ss1751936529, ss1917720784, ss1945981603, ss1958230156, ss2730986987, ss2746169475, ss2750649467, ss2984841004, ss3021043175, ss3626006652, ss3634301831, ss3640009197, ss3644477474, ss3651365227, ss3653614754, ss3744337210, ss3744602763, ss3772104528, ss3823541303, ss5847521225, ss5936584112, ss5979259803 NC_000001.10:866428:C:T NC_000001.11:931048:C:T (self)
RCV001213858.5, 87431, 33, 64748, 546171005, ss2159370806, ss3724988118, ss3770778564, ss4436458413 NC_000001.11:931048:C:T NC_000001.11:931048: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 rs144317111

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.post761+d5e8e07