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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs112422281

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:943273 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.001160 (307/264690, TOPMED)
G=0.000238 (59/247526, GnomAD_exome)
G=0.001034 (145/140180, GnomAD) (+ 6 more)
G=0.000272 (31/113806, ExAC)
G=0.00027 (14/51180, ALFA)
G=0.00131 (17/13002, GO-ESP)
G=0.0012 (8/6404, 1000G_30x)
G=0.0012 (6/5008, 1000G)
A=0.3 (2/6, SGDP_PRJ)
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: 20231103111315
Population Group Sample Size Ref Allele Alt Allele Ref HMOZ Alt HMOZ HTRZ HWEP
Total Global 67540 A=0.99953 G=0.00047 0.999052 0.0 0.000948 0
European Sub 49012 A=1.00000 G=0.00000 1.0 0.0 0.0 N/A
African Sub 8398 A=0.9963 G=0.0037 0.992617 0.0 0.007383 0
African Others Sub 306 A=0.993 G=0.007 0.986928 0.0 0.013072 0
African American Sub 8092 A=0.9964 G=0.0036 0.992832 0.0 0.007168 0
Asian Sub 168 A=1.000 G=0.000 1.0 0.0 0.0 N/A
East Asian Sub 112 A=1.000 G=0.000 1.0 0.0 0.0 N/A
Other Asian Sub 56 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Latin American 1 Sub 500 A=0.998 G=0.002 0.996 0.0 0.004 0
Latin American 2 Sub 628 A=1.000 G=0.000 1.0 0.0 0.0 N/A
South Asian Sub 98 A=1.00 G=0.00 1.0 0.0 0.0 N/A
Other Sub 8736 A=1.0000 G=0.0000 1.0 0.0 0.0 N/A


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 A=0.998840 G=0.001160
gnomAD - Exomes Global Study-wide 247526 A=0.999762 G=0.000238
gnomAD - Exomes European Sub 132550 A=1.000000 G=0.000000
gnomAD - Exomes Asian Sub 48860 A=1.00000 G=0.00000
gnomAD - Exomes American Sub 34396 A=0.99991 G=0.00009
gnomAD - Exomes African Sub 15756 A=0.99651 G=0.00349
gnomAD - Exomes Ashkenazi Jewish Sub 9934 A=1.0000 G=0.0000
gnomAD - Exomes Other Sub 6030 A=0.9998 G=0.0002
gnomAD - Genomes Global Study-wide 140180 A=0.998966 G=0.001034
gnomAD - Genomes European Sub 75894 A=1.00000 G=0.00000
gnomAD - Genomes African Sub 42026 A=0.99662 G=0.00338
gnomAD - Genomes American Sub 13664 A=0.99985 G=0.00015
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3122 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2152 A=0.9995 G=0.0005
ExAC Global Study-wide 113806 A=0.999728 G=0.000272
ExAC Europe Sub 68078 A=1.00000 G=0.00000
ExAC Asian Sub 24408 A=1.00000 G=0.00000
ExAC American Sub 11136 A=1.00000 G=0.00000
ExAC African Sub 9374 A=0.9967 G=0.0033
ExAC Other Sub 810 A=1.000 G=0.000
Allele Frequency Aggregator Total Global 51180 A=0.99973 G=0.00027
Allele Frequency Aggregator European Sub 38924 A=1.00000 G=0.00000
Allele Frequency Aggregator Other Sub 7302 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 3560 A=0.9963 G=0.0037
Allele Frequency Aggregator Latin American 2 Sub 628 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 A=0.998 G=0.002
Allele Frequency Aggregator Asian Sub 168 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 13002 A=0.99869 G=0.00131
GO Exome Sequencing Project European American Sub 8600 A=1.0000 G=0.0000
GO Exome Sequencing Project African American Sub 4402 A=0.9961 G=0.0039
1000Genomes_30x Global Study-wide 6404 A=0.9988 G=0.0012
1000Genomes_30x African Sub 1786 A=0.9955 G=0.0045
1000Genomes_30x Europe Sub 1266 A=1.0000 G=0.0000
1000Genomes_30x South Asian Sub 1202 A=1.0000 G=0.0000
1000Genomes_30x East Asian Sub 1170 A=1.0000 G=0.0000
1000Genomes_30x American Sub 980 A=1.000 G=0.000
1000Genomes Global Study-wide 5008 A=0.9988 G=0.0012
1000Genomes African Sub 1322 A=0.9955 G=0.0045
1000Genomes East Asian Sub 1008 A=1.0000 G=0.0000
1000Genomes Europe Sub 1006 A=1.0000 G=0.0000
1000Genomes South Asian Sub 978 A=1.000 G=0.000
1000Genomes American Sub 694 A=1.000 G=0.000
SGDP_PRJ Global Study-wide 6 A=0.3 G=0.7
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.943273A>G
GRCh37.p13 chr 1 NC_000001.10:g.878653A>G
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.1585A>G M [ATG] > V [GTG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Met529Val M (Met) > V (Val) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.2074A>G M [ATG] > V [GTG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Met692Val M (Met) > V (Val) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.2077A>G M [ATG] > V [GTG] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Met693Val M (Met) > V (Val) 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: G (allele ID: 1131801 )
ClinVar Accession Disease Names Clinical Significance
RCV001491848.4 not provided Likely-Benign
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 A= G
GRCh38.p14 chr 1 NC_000001.11:g.943273= NC_000001.11:g.943273A>G
GRCh37.p13 chr 1 NC_000001.10:g.878653= NC_000001.10:g.878653A>G
SAMD11 transcript variant 3 NM_152486.4:c.1585= NM_152486.4:c.1585A>G
SAMD11 transcript NM_152486.3:c.1585= NM_152486.3:c.1585A>G
SAMD11 transcript NM_152486.2:c.1585= NM_152486.2:c.1585A>G
SAMD11 transcript variant 2 NM_001385640.1:c.2077= NM_001385640.1:c.2077A>G
SAMD11 transcript variant 1 NM_001385641.1:c.2074= NM_001385641.1:c.2074A>G
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Met529= NP_689699.3:p.Met529Val
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Met693= NP_001372569.1:p.Met693Val
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Met692= NP_001372570.1:p.Met692Val
sterile alpha motif domain-containing protein 11 NP_689699.2:p.Met529= NP_689699.2:p.Met529Val
SAMD11 transcript variant X5 XM_005244727.1:c.659-425= XM_005244727.1:c.659-425A>G
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#.

22 SubSNP, 9 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 BUSHMAN ss197886500 Jul 04, 2010 (132)
2 NHLBI-ESP ss341923380 May 09, 2011 (134)
3 EXOME_CHIP ss491283815 May 04, 2012 (137)
4 JMKIDD_LAB ss1067414253 Aug 21, 2014 (142)
5 JMKIDD_LAB ss1067612787 Aug 21, 2014 (142)
6 1000GENOMES ss1289343144 Aug 21, 2014 (142)
7 EVA_EXAC ss1685217940 Apr 01, 2015 (144)
8 HUMAN_LONGEVITY ss2159372043 Dec 20, 2016 (150)
9 GNOMAD ss2730987893 Nov 08, 2017 (151)
10 GNOMAD ss2746169824 Nov 08, 2017 (151)
11 GNOMAD ss2750651203 Nov 08, 2017 (151)
12 AFFY ss2984841018 Nov 08, 2017 (151)
13 ILLUMINA ss3653614770 Oct 11, 2018 (152)
14 KHV_HUMAN_GENOMES ss3798744794 Jul 12, 2019 (153)
15 EVA ss3823541397 Apr 25, 2020 (154)
16 SGDP_PRJ ss3847998733 Apr 25, 2020 (154)
17 TOPMED ss4436463384 Apr 25, 2021 (155)
18 1000G_HIGH_COVERAGE ss5240867113 Oct 12, 2022 (156)
19 EVA ss5316189420 Oct 12, 2022 (156)
20 HUGCELL_USP ss5442114822 Oct 12, 2022 (156)
21 1000G_HIGH_COVERAGE ss5512493178 Oct 12, 2022 (156)
22 EVA ss5906707901 Oct 12, 2022 (156)
23 1000Genomes NC_000001.10 - 878653 Oct 11, 2018 (152)
24 1000Genomes_30x NC_000001.11 - 943273 Oct 12, 2022 (156)
25 ExAC NC_000001.10 - 878653 Oct 11, 2018 (152)
26 gnomAD - Genomes NC_000001.11 - 943273 Apr 25, 2021 (155)
27 gnomAD - Exomes NC_000001.10 - 878653 Jul 12, 2019 (153)
28 GO Exome Sequencing Project NC_000001.10 - 878653 Oct 11, 2018 (152)
29 SGDP_PRJ NC_000001.10 - 878653 Apr 25, 2020 (154)
30 TopMed NC_000001.11 - 943273 Apr 25, 2021 (155)
31 ALFA NC_000001.11 - 943273 Apr 25, 2021 (155)
32 ClinVar RCV001491848.4 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
ss197886500 NC_000001.9:868515:A:G NC_000001.11:943272:A:G (self)
8031, 4391083, 2116, 134, 15713, ss341923380, ss491283815, ss1067414253, ss1067612787, ss1289343144, ss1685217940, ss2730987893, ss2746169824, ss2750651203, ss2984841018, ss3653614770, ss3823541397, ss3847998733, ss5316189420 NC_000001.10:878652:A:G NC_000001.11:943272:A:G (self)
RCV001491848.4, 19113, 91683, 69719, 10430139619, ss2159372043, ss3798744794, ss4436463384, ss5240867113, ss5442114822, ss5512493178, ss5906707901 NC_000001.11:943272:A:G NC_000001.11:943272:A:G (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 rs112422281

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.post825+45319f0