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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.

rs5772025

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr1:932614-932621 (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
delTTTC
Variation Type
Indel Insertion and Deletion
Frequency
(TTTC)2=0.173682 (45972/264690, TOPMED)
(TTTC)2=0.166500 (23307/139982, GnomAD)
(TTTC)2=0.00014 (4/28256, 14KJPN) (+ 10 more)
(TTTC)2=0.09460 (1752/18520, ALFA)
(TTTC)2=0.00006 (1/16758, 8.3KJPN)
(TTTC)2=0.1790 (1146/6404, 1000G_30x)
(TTTC)2=0.0085 (38/4480, Estonian)
(TTTC)2=0.0052 (20/3854, ALSPAC)
(TTTC)2=0.0092 (34/3708, TWINSUK)
(TTTC)2=0.0000 (0/1832, Korea1K)
(TTTC)2=0.006 (6/998, GoNL)
(TTTC)2=0.005 (3/600, NorthernSweden)
(TTTC)2=0.023 (5/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
SAMD11 : Intron 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 18520 TTTCTTTC=0.09460 TTTC=0.90540
European Sub 14152 TTTCTTTC=0.00848 TTTC=0.99152
African Sub 2898 TTTCTTTC=0.5200 TTTC=0.4800
African Others Sub 114 TTTCTTTC=0.614 TTTC=0.386
African American Sub 2784 TTTCTTTC=0.5162 TTTC=0.4838
Asian Sub 112 TTTCTTTC=0.000 TTTC=1.000
East Asian Sub 86 TTTCTTTC=0.00 TTTC=1.00
Other Asian Sub 26 TTTCTTTC=0.00 TTTC=1.00
Latin American 1 Sub 146 TTTCTTTC=0.171 TTTC=0.829
Latin American 2 Sub 610 TTTCTTTC=0.031 TTTC=0.969
South Asian Sub 98 TTTCTTTC=0.00 TTTC=1.00
Other Sub 504 TTTCTTTC=0.161 TTTC=0.839


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 (TTTC)2=0.173682 delTTTC=0.826318
gnomAD - Genomes Global Study-wide 139982 (TTTC)2=0.166500 delTTTC=0.833500
gnomAD - Genomes European Sub 75876 (TTTC)2=0.00830 delTTTC=0.99170
gnomAD - Genomes African Sub 41854 (TTTC)2=0.51271 delTTTC=0.48729
gnomAD - Genomes American Sub 13656 (TTTC)2=0.06503 delTTTC=0.93497
gnomAD - Genomes Ashkenazi Jewish Sub 3320 (TTTC)2=0.0075 delTTTC=0.9925
gnomAD - Genomes East Asian Sub 3128 (TTTC)2=0.0003 delTTTC=0.9997
gnomAD - Genomes Other Sub 2148 (TTTC)2=0.1415 delTTTC=0.8585
14KJPN JAPANESE Study-wide 28256 (TTTC)2=0.00014 delTTTC=0.99986
Allele Frequency Aggregator Total Global 18520 (TTTC)2=0.09460 delTTTC=0.90540
Allele Frequency Aggregator European Sub 14152 (TTTC)2=0.00848 delTTTC=0.99152
Allele Frequency Aggregator African Sub 2898 (TTTC)2=0.5200 delTTTC=0.4800
Allele Frequency Aggregator Latin American 2 Sub 610 (TTTC)2=0.031 delTTTC=0.969
Allele Frequency Aggregator Other Sub 504 (TTTC)2=0.161 delTTTC=0.839
Allele Frequency Aggregator Latin American 1 Sub 146 (TTTC)2=0.171 delTTTC=0.829
Allele Frequency Aggregator Asian Sub 112 (TTTC)2=0.000 delTTTC=1.000
Allele Frequency Aggregator South Asian Sub 98 (TTTC)2=0.00 delTTTC=1.00
8.3KJPN JAPANESE Study-wide 16758 (TTTC)2=0.00006 delTTTC=0.99994
1000Genomes_30x Global Study-wide 6404 (TTTC)2=0.1790 delTTTC=0.8210
1000Genomes_30x African Sub 1786 (TTTC)2=0.6013 delTTTC=0.3987
1000Genomes_30x Europe Sub 1266 (TTTC)2=0.0095 delTTTC=0.9905
1000Genomes_30x South Asian Sub 1202 (TTTC)2=0.0017 delTTTC=0.9983
1000Genomes_30x East Asian Sub 1170 (TTTC)2=0.0017 delTTTC=0.9983
1000Genomes_30x American Sub 980 (TTTC)2=0.057 delTTTC=0.943
Genetic variation in the Estonian population Estonian Study-wide 4480 (TTTC)2=0.0085 delTTTC=0.9915
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 (TTTC)2=0.0052 delTTTC=0.9948
UK 10K study - Twins TWIN COHORT Study-wide 3708 (TTTC)2=0.0092 delTTTC=0.9908
Korean Genome Project KOREAN Study-wide 1832 (TTTC)2=0.0000 delTTTC=1.0000
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 (TTTC)2=0.006 delTTTC=0.994
Northern Sweden ACPOP Study-wide 600 (TTTC)2=0.005 delTTTC=0.995
A Vietnamese Genetic Variation Database Global Study-wide 214 (TTTC)2=0.023 delTTTC=0.977
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.932614TTTC[1]
GRCh37.p13 chr 1 NC_000001.10:g.867994TTTC[1]
Gene: SAMD11, sterile alpha motif domain containing 11 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
SAMD11 transcript variant 2 NM_001385640.1:c.842+1529…

NM_001385640.1:c.842+1529_842+1532del

N/A Intron Variant
SAMD11 transcript variant 1 NM_001385641.1:c.842+1529…

NM_001385641.1:c.842+1529_842+1532del

N/A Intron Variant
SAMD11 transcript variant 3 NM_152486.4:c.305+1529_30…

NM_152486.4:c.305+1529_305+1532del

N/A Intron 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
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 (TTTC)2= delTTTC
GRCh38.p14 chr 1 NC_000001.11:g.932614_932621= NC_000001.11:g.932614TTTC[1]
GRCh37.p13 chr 1 NC_000001.10:g.867994_868001= NC_000001.10:g.867994TTTC[1]
SAMD11 transcript variant 2 NM_001385640.1:c.842+1525= NM_001385640.1:c.842+1529_842+1532del
SAMD11 transcript variant 1 NM_001385641.1:c.842+1525= NM_001385641.1:c.842+1529_842+1532del
SAMD11 transcript NM_152486.2:c.305+1525= NM_152486.2:c.305+1529_305+1532del
SAMD11 transcript variant 3 NM_152486.4:c.305+1525= NM_152486.4:c.305+1529_305+1532del
SAMD11 transcript variant X1 XM_005244723.1:c.305+1525= XM_005244723.1:c.305+1529_305+1532del
SAMD11 transcript variant X2 XM_005244724.1:c.305+1525= XM_005244724.1:c.305+1529_305+1532del
SAMD11 transcript variant X3 XM_005244725.1:c.305+1525= XM_005244725.1:c.305+1529_305+1532del
SAMD11 transcript variant X4 XM_005244726.1:c.305+1525= XM_005244726.1:c.305+1529_305+1532del
SAMD11 transcript variant X5 XM_005244727.1:c.305+1525= XM_005244727.1:c.305+1529_305+1532del
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#.

58 SubSNP, 13 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss4310868 Mar 15, 2016 (147)
2 HGSV ss77880247 Sep 08, 2015 (146)
3 HGSV ss82789852 Sep 08, 2015 (146)
4 HGSV ss82841750 Sep 08, 2015 (146)
5 HUMANGENOME_JCVI ss95218910 Dec 03, 2013 (138)
6 BCMHGSC_JDW ss103475676 Dec 06, 2013 (138)
7 GMI ss154521633 Mar 15, 2016 (147)
8 GMI ss229263689 Mar 15, 2016 (147)
9 BL ss255892680 May 09, 2011 (137)
10 GMI ss287939418 May 04, 2012 (137)
11 PJP ss294562353 Aug 21, 2014 (142)
12 PJP ss294562354 May 09, 2011 (135)
13 1000GENOMES ss325997571 May 09, 2011 (137)
14 LUNTER ss550899173 Apr 25, 2013 (138)
15 LUNTER ss550903160 Apr 25, 2013 (138)
16 LUNTER ss552739065 Apr 25, 2013 (138)
17 TISHKOFF ss553708546 Apr 25, 2013 (138)
18 SSMP ss663211381 Apr 01, 2015 (144)
19 BILGI_BIOE ss666080094 Apr 25, 2013 (138)
20 EVA-GONL ss974770218 Aug 21, 2014 (142)
21 DDI ss1536213911 Apr 01, 2015 (144)
22 EVA_DECODE ss1584130134 Apr 01, 2015 (144)
23 EVA_UK10K_ALSPAC ss1700143862 Apr 01, 2015 (144)
24 EVA_UK10K_TWINSUK ss1700153958 Apr 01, 2015 (144)
25 HAMMER_LAB ss1793710229 Sep 08, 2015 (146)
26 JJLAB ss2030297787 Sep 14, 2016 (149)
27 SYSTEMSBIOZJU ss2624264989 Nov 08, 2017 (151)
28 GNOMAD ss2750649659 Nov 08, 2017 (151)
29 SWEGEN ss2986151124 Nov 08, 2017 (151)
30 MCHAISSO ss3063573549 Nov 08, 2017 (151)
31 MCHAISSO ss3064386070 Nov 08, 2017 (151)
32 MCHAISSO ss3065282553 Nov 08, 2017 (151)
33 BEROUKHIMLAB ss3644051509 Oct 11, 2018 (152)
34 BIOINF_KMB_FNS_UNIBA ss3645022435 Oct 11, 2018 (152)
35 URBANLAB ss3646581415 Oct 11, 2018 (152)
36 EGCUT_WGS ss3654262411 Jul 12, 2019 (153)
37 EVA_DECODE ss3685993750 Jul 12, 2019 (153)
38 ACPOP ss3726717068 Jul 12, 2019 (153)
39 PACBIO ss3783302555 Jul 12, 2019 (153)
40 PACBIO ss3788980216 Jul 12, 2019 (153)
41 PACBIO ss3793852776 Jul 12, 2019 (153)
42 KHV_HUMAN_GENOMES ss3798744647 Jul 12, 2019 (153)
43 EVA ss3825981792 Apr 25, 2020 (154)
44 EVA ss3836378601 Apr 25, 2020 (154)
45 EVA ss3841782620 Apr 25, 2020 (154)
46 KOGIC ss3943631753 Apr 25, 2020 (154)
47 TOPMED ss4436458943 Apr 25, 2021 (155)
48 TOMMO_GENOMICS ss5142057059 Apr 25, 2021 (155)
49 1000G_HIGH_COVERAGE ss5240866640 Oct 12, 2022 (156)
50 HUGCELL_USP ss5442114404 Oct 12, 2022 (156)
51 1000G_HIGH_COVERAGE ss5512492516 Oct 12, 2022 (156)
52 SANFORD_IMAGENETICS ss5624751567 Oct 12, 2022 (156)
53 TOMMO_GENOMICS ss5666197957 Oct 12, 2022 (156)
54 YY_MCH ss5800244702 Oct 12, 2022 (156)
55 EVA ss5831419811 Oct 12, 2022 (156)
56 EVA ss5848749142 Oct 12, 2022 (156)
57 EVA ss5906707420 Oct 12, 2022 (156)
58 EVA ss5936584156 Oct 12, 2022 (156)
59 1000Genomes_30x NC_000001.11 - 932614 Oct 12, 2022 (156)
60 The Avon Longitudinal Study of Parents and Children NC_000001.10 - 867994 Oct 11, 2018 (152)
61 Genetic variation in the Estonian population NC_000001.10 - 867994 Oct 11, 2018 (152)
62 gnomAD - Genomes NC_000001.11 - 932614 Apr 25, 2021 (155)
63 Genome of the Netherlands Release 5 NC_000001.10 - 867994 Apr 25, 2020 (154)
64 Korean Genome Project NC_000001.11 - 932614 Apr 25, 2020 (154)
65 Northern Sweden NC_000001.10 - 867994 Jul 12, 2019 (153)
66 8.3KJPN NC_000001.10 - 867994 Apr 25, 2021 (155)
67 14KJPN NC_000001.11 - 932614 Oct 12, 2022 (156)
68 TopMed NC_000001.11 - 932614 Apr 25, 2021 (155)
69 UK 10K study - Twins NC_000001.10 - 867994 Oct 11, 2018 (152)
70 A Vietnamese Genetic Variation Database NC_000001.10 - 867994 Jul 12, 2019 (153)
71 ALFA NC_000001.11 - 932614 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).

Associated ID History Updated (Build)
rs33981253 Oct 16, 2006 (127)
rs58302334 May 24, 2008 (130)
rs138211850 May 11, 2012 (137)
rs143415364 Sep 17, 2011 (135)
rs374903126 May 15, 2013 (138)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77880247, ss82789852, ss82841750 NC_000001.8:907860:TTTC: NC_000001.11:932613:TTTCTTTC:TTTC (self)
ss255892680, ss287939418, ss294562353, ss325997571, ss550899173, ss550903160, ss552739065, ss1584130134 NC_000001.9:857856:TTTC: NC_000001.11:932613:TTTCTTTC:TTTC (self)
ss294562354 NC_000001.9:857860:TTTC: NC_000001.11:932613:TTTCTTTC:TTTC (self)
1552, 659, 1129, 1933, 26366, 1552, 347, ss663211381, ss666080094, ss974770218, ss1536213911, ss1700143862, ss1700153958, ss1793710229, ss2030297787, ss2624264989, ss2750649659, ss2986151124, ss3644051509, ss3654262411, ss3726717068, ss3783302555, ss3788980216, ss3793852776, ss3825981792, ss3836378601, ss5142057059, ss5624751567, ss5831419811, ss5936584156 NC_000001.10:867993:TTTC: NC_000001.11:932613:TTTCTTTC:TTTC (self)
ss553708546 NC_000001.10:867997:TTTC: NC_000001.11:932613:TTTCTTTC:TTTC (self)
18451, 87886, 9754, 35061, 65278, ss3063573549, ss3064386070, ss3065282553, ss3645022435, ss3646581415, ss3685993750, ss3798744647, ss3841782620, ss3943631753, ss4436458943, ss5240866640, ss5442114404, ss5512492516, ss5666197957, ss5800244702, ss5848749142, ss5906707420 NC_000001.11:932613:TTTC: NC_000001.11:932613:TTTCTTTC:TTTC (self)
12908585422 NC_000001.11:932613:TTTCTTTC:TTTC NC_000001.11:932613:TTTCTTTC:TTTC (self)
ss4310868, ss154521633, ss229263689 NT_004350.19:346625:TTTC: NC_000001.11:932613:TTTCTTTC:TTTC (self)
ss95218910, ss103475676 NT_004350.19:346629:TTTC: NC_000001.11:932613:TTTCTTTC:TTTC (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 rs5772025

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