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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.

rs149677938

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:939076 (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
A=0.00015 (12/81116, ALFA)
A=0.00139 (109/78684, PAGE_STUDY)
A=0.00131 (17/13002, GO-ESP) (+ 3 more)
A=0.0010 (5/5008, 1000G)
G=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)
Clinical Significance
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.939076G>A
GRCh38.p13 chr 1 NC_000001.11:g.939076G>C
GRCh38.p13 chr 1 NC_000001.11:g.939076G>T
GRCh37.p13 chr 1 NC_000001.10:g.874456G>A
GRCh37.p13 chr 1 NC_000001.10:g.874456G>C
GRCh37.p13 chr 1 NC_000001.10:g.874456G>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.467G>A R [CGT] > H [CAT] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Arg156His R (Arg) > H (His) Missense Variant
SAMD11 transcript variant 3 NM_152486.4:c.467G>C R [CGT] > P [CCT] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Arg156Pro R (Arg) > P (Pro) Missense Variant
SAMD11 transcript variant 3 NM_152486.4:c.467G>T R [CGT] > L [CTT] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Arg156Leu R (Arg) > L (Leu) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.1004G>A R [CGT] > H [CAT] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Arg335His R (Arg) > H (His) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.1004G>C R [CGT] > P [CCT] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Arg335Pro R (Arg) > P (Pro) Missense Variant
SAMD11 transcript variant 1 NM_001385641.1:c.1004G>T R [CGT] > L [CTT] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Arg335Leu R (Arg) > L (Leu) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.1004G>A R [CGT] > H [CAT] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Arg335His R (Arg) > H (His) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.1004G>C R [CGT] > P [CCT] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Arg335Pro R (Arg) > P (Pro) Missense Variant
SAMD11 transcript variant 2 NM_001385640.1:c.1004G>T R [CGT] > L [CTT] Coding Sequence Variant
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Arg335Leu R (Arg) > 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.

Allele: T (allele ID: 824444 )
ClinVar Accession Disease Names Clinical Significance
RCV001060627.2 not provided Uncertain-Significance

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 81116 G=0.99985 A=0.00015, C=0.00000, T=0.00000
European Sub 65712 G=0.99992 A=0.00008, C=0.00000, T=0.00000
African Sub 4120 G=0.9983 A=0.0017, C=0.0000, T=0.0000
African Others Sub 122 G=1.000 A=0.000, C=0.000, T=0.000
African American Sub 3998 G=0.9982 A=0.0018, C=0.0000, T=0.0000
Asian Sub 3158 G=1.0000 A=0.0000, C=0.0000, T=0.0000
East Asian Sub 1924 G=1.0000 A=0.0000, C=0.0000, T=0.0000
Other Asian Sub 1234 G=1.0000 A=0.0000, C=0.0000, T=0.0000
Latin American 1 Sub 152 G=1.000 A=0.000, C=0.000, T=0.000
Latin American 2 Sub 632 G=1.000 A=0.000, C=0.000, T=0.000
South Asian Sub 104 G=1.000 A=0.000, C=0.000, T=0.000
Other Sub 7238 G=1.0000 A=0.0000, C=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
The PAGE Study Global Study-wide 78684 G=0.99861 A=0.00139
The PAGE Study AfricanAmerican Sub 32504 G=0.99711 A=0.00289
The PAGE Study Mexican Sub 10810 G=0.99991 A=0.00009
The PAGE Study Asian Sub 8318 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7916 G=0.9994 A=0.0006
The PAGE Study NativeHawaiian Sub 4532 G=0.9998 A=0.0002
The PAGE Study Cuban Sub 4228 G=0.9988 A=0.0012
The PAGE Study Dominican Sub 3828 G=0.9997 A=0.0003
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=0.9995 A=0.0005
The PAGE Study NativeAmerican Sub 1260 G=0.9992 A=0.0008
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
GO Exome Sequencing Project Global Study-wide 13002 G=0.99869 A=0.00131
GO Exome Sequencing Project European American Sub 8600 G=0.9999 A=0.0001
GO Exome Sequencing Project African American Sub 4402 G=0.9964 A=0.0036
1000Genomes Global Study-wide 5008 G=0.9990 A=0.0010
1000Genomes African Sub 1322 G=0.9962 A=0.0038
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=1.0000 A=0.0000
1000Genomes South Asian Sub 978 G=1.000 A=0.000
1000Genomes American Sub 694 G=1.000 A=0.000
SGDP_PRJ Global Study-wide 2 G=0.5 A=0.5
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.939076= NC_000001.11:g.939076G>A NC_000001.11:g.939076G>C NC_000001.11:g.939076G>T
GRCh37.p13 chr 1 NC_000001.10:g.874456= NC_000001.10:g.874456G>A NC_000001.10:g.874456G>C NC_000001.10:g.874456G>T
SAMD11 transcript variant 3 NM_152486.4:c.467= NM_152486.4:c.467G>A NM_152486.4:c.467G>C NM_152486.4:c.467G>T
SAMD11 transcript NM_152486.3:c.467= NM_152486.3:c.467G>A NM_152486.3:c.467G>C NM_152486.3:c.467G>T
SAMD11 transcript NM_152486.2:c.467= NM_152486.2:c.467G>A NM_152486.2:c.467G>C NM_152486.2:c.467G>T
SAMD11 transcript variant 2 NM_001385640.1:c.1004= NM_001385640.1:c.1004G>A NM_001385640.1:c.1004G>C NM_001385640.1:c.1004G>T
SAMD11 transcript variant 1 NM_001385641.1:c.1004= NM_001385641.1:c.1004G>A NM_001385641.1:c.1004G>C NM_001385641.1:c.1004G>T
sterile alpha motif domain-containing protein 11 isoform 3 NP_689699.3:p.Arg156= NP_689699.3:p.Arg156His NP_689699.3:p.Arg156Pro NP_689699.3:p.Arg156Leu
sterile alpha motif domain-containing protein 11 isoform 2 NP_001372569.1:p.Arg335= NP_001372569.1:p.Arg335His NP_001372569.1:p.Arg335Pro NP_001372569.1:p.Arg335Leu
sterile alpha motif domain-containing protein 11 isoform 1 NP_001372570.1:p.Arg335= NP_001372570.1:p.Arg335His NP_001372570.1:p.Arg335Pro NP_001372570.1:p.Arg335Leu
sterile alpha motif domain-containing protein 11 NP_689699.2:p.Arg156= NP_689699.2:p.Arg156His NP_689699.2:p.Arg156Pro NP_689699.2:p.Arg156Leu
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#.

38 SubSNP, 15 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss341923361 May 09, 2011 (134)
2 1000GENOMES ss487561431 May 04, 2012 (137)
3 EXOME_CHIP ss491283800 May 04, 2012 (137)
4 ILLUMINA ss780893389 Sep 08, 2015 (146)
5 ILLUMINA ss783580024 Sep 08, 2015 (146)
6 JMKIDD_LAB ss1067414242 Aug 21, 2014 (142)
7 1000GENOMES ss1289342959 Aug 21, 2014 (142)
8 EVA_EXAC ss1685217482 Apr 01, 2015 (144)
9 EVA_EXAC ss1685217483 Apr 01, 2015 (144)
10 ILLUMINA ss1751936831 Sep 08, 2015 (146)
11 ILLUMINA ss1917720789 Feb 12, 2016 (147)
12 ILLUMINA ss1945981608 Feb 12, 2016 (147)
13 ILLUMINA ss1958230182 Feb 12, 2016 (147)
14 HUMAN_LONGEVITY ss2159371550 Dec 20, 2016 (150)
15 TOPMED ss2321510324 Dec 20, 2016 (150)
16 TOPMED ss2321510325 Dec 20, 2016 (150)
17 GNOMAD ss2730987168 Nov 08, 2017 (151)
18 GNOMAD ss2746169536 Nov 08, 2017 (151)
19 GNOMAD ss2750650507 Nov 08, 2017 (151)
20 ILLUMINA ss3021043197 Nov 08, 2017 (151)
21 TOPMED ss3066424075 Nov 08, 2017 (151)
22 TOPMED ss3066424076 Nov 08, 2017 (151)
23 TOPMED ss3066424077 Nov 08, 2017 (151)
24 ILLUMINA ss3626006676 Oct 11, 2018 (152)
25 ILLUMINA ss3634301838 Oct 11, 2018 (152)
26 ILLUMINA ss3640009204 Oct 11, 2018 (152)
27 ILLUMINA ss3644477480 Oct 11, 2018 (152)
28 ILLUMINA ss3651365249 Oct 11, 2018 (152)
29 ILLUMINA ss3724988132 Jul 12, 2019 (153)
30 ILLUMINA ss3744337215 Jul 12, 2019 (153)
31 ILLUMINA ss3744602770 Jul 12, 2019 (153)
32 PAGE_CC ss3770778579 Jul 12, 2019 (153)
33 ILLUMINA ss3772104534 Jul 12, 2019 (153)
34 EVA ss3823541339 Apr 25, 2020 (154)
35 SGDP_PRJ ss3847998626 Apr 25, 2020 (154)
36 TOPMED ss4436461272 Apr 25, 2021 (155)
37 TOPMED ss4436461273 Apr 25, 2021 (155)
38 TOPMED ss4436461274 Apr 25, 2021 (155)
39 1000Genomes NC_000001.10 - 874456 Oct 11, 2018 (152)
40 ExAC

Submission ignored due to conflicting rows:
Row 4390594 (NC_000001.10:874455:G:G 60144/60170, NC_000001.10:874455:G:A 26/60170)
Row 4390595 (NC_000001.10:874455:G:G 60167/60170, NC_000001.10:874455:G:T 3/60170)

- Oct 11, 2018 (152)
41 ExAC

Submission ignored due to conflicting rows:
Row 4390594 (NC_000001.10:874455:G:G 60144/60170, NC_000001.10:874455:G:A 26/60170)
Row 4390595 (NC_000001.10:874455:G:G 60167/60170, NC_000001.10:874455:G:T 3/60170)

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

Submission ignored due to conflicting rows:
Row 89885 (NC_000001.11:939075:G:A 125/140238)
Row 89886 (NC_000001.11:939075:G:T 3/140238)

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

Submission ignored due to conflicting rows:
Row 89885 (NC_000001.11:939075:G:A 125/140238)
Row 89886 (NC_000001.11:939075:G:T 3/140238)

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

Submission ignored due to conflicting rows:
Row 1534 (NC_000001.10:874455:G:G 235392/235446, NC_000001.10:874455:G:A 54/235446)
Row 1535 (NC_000001.10:874455:G:G 235445/235446, NC_000001.10:874455:G:C 1/235446)
Row 1536 (NC_000001.10:874455:G:G 235444/235446, NC_000001.10:874455:G:T 2/235446)

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

Submission ignored due to conflicting rows:
Row 1534 (NC_000001.10:874455:G:G 235392/235446, NC_000001.10:874455:G:A 54/235446)
Row 1535 (NC_000001.10:874455:G:G 235445/235446, NC_000001.10:874455:G:C 1/235446)
Row 1536 (NC_000001.10:874455:G:G 235444/235446, NC_000001.10:874455:G:T 2/235446)

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

Submission ignored due to conflicting rows:
Row 1534 (NC_000001.10:874455:G:G 235392/235446, NC_000001.10:874455:G:A 54/235446)
Row 1535 (NC_000001.10:874455:G:G 235445/235446, NC_000001.10:874455:G:C 1/235446)
Row 1536 (NC_000001.10:874455:G:G 235444/235446, NC_000001.10:874455:G:T 2/235446)

- Jul 12, 2019 (153)
47 GO Exome Sequencing Project NC_000001.10 - 874456 Oct 11, 2018 (152)
48 The PAGE Study NC_000001.11 - 939076 Jul 12, 2019 (153)
49 SGDP_PRJ NC_000001.10 - 874456 Apr 25, 2020 (154)
50 TopMed

Submission ignored due to conflicting rows:
Row 67607 (NC_000001.11:939075:G:A 263/264690)
Row 67608 (NC_000001.11:939075:G:C 3/264690)
Row 67609 (NC_000001.11:939075:G:T 3/264690)

- Apr 25, 2021 (155)
51 TopMed

Submission ignored due to conflicting rows:
Row 67607 (NC_000001.11:939075:G:A 263/264690)
Row 67608 (NC_000001.11:939075:G:C 3/264690)
Row 67609 (NC_000001.11:939075:G:T 3/264690)

- Apr 25, 2021 (155)
52 TopMed

Submission ignored due to conflicting rows:
Row 67607 (NC_000001.11:939075:G:A 263/264690)
Row 67608 (NC_000001.11:939075:G:C 3/264690)
Row 67609 (NC_000001.11:939075:G:T 3/264690)

- Apr 25, 2021 (155)
53 ALFA NC_000001.11 - 939076 Apr 25, 2021 (155)
54 ClinVar RCV001060627.2 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
7838, 76, 15606, ss341923361, ss487561431, ss491283800, ss780893389, ss783580024, ss1067414242, ss1289342959, ss1685217482, ss1751936831, ss1917720789, ss1945981608, ss1958230182, ss2321510324, ss2730987168, ss2746169536, ss2750650507, ss3021043197, ss3626006676, ss3634301838, ss3640009204, ss3644477480, ss3651365249, ss3744337215, ss3744602770, ss3772104534, ss3823541339, ss3847998626 NC_000001.10:874455:G:A NC_000001.11:939075:G:A (self)
48, 34424, 10016845061, ss2159371550, ss3066424075, ss3724988132, ss3770778579, ss4436461272 NC_000001.11:939075:G:A NC_000001.11:939075:G:A (self)
ss2321510325, ss2730987168 NC_000001.10:874455:G:C NC_000001.11:939075:G:C (self)
34424, 10016845061, ss3066424076, ss4436461273 NC_000001.11:939075:G:C NC_000001.11:939075:G:C (self)
ss1685217483, ss2730987168 NC_000001.10:874455:G:T NC_000001.11:939075:G:T (self)
RCV001060627.2, 34424, 10016845061, ss2159371550, ss3066424077, ss4436461274 NC_000001.11:939075:G:T NC_000001.11:939075: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 rs149677938

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