Name: rs55678698
Published: September 21, 2022
License: Open Access

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.

rs55678698

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr1:929110 (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=0.026450 (7001/264690, TOPMED)
T=0.028710 (4027/140264, GnomAD)
T=0.03430 (877/25570, ALFA) (+ 13 more)
T=0.0198 (127/6404, 1000G_30x)
T=0.0196 (98/5008, 1000G)
T=0.0342 (153/4480, Estonian)
T=0.0361 (139/3854, ALSPAC)
T=0.0332 (123/3708, TWINSUK)
T=0.050 (50/998, GoNL)
T=0.020 (12/600, NorthernSweden)
T=0.028 (6/216, Qatari)
T=0.03 (1/40, GENOME_DK)
C=0.50 (9/18, SGDP_PRJ)
T=0.50 (9/18, SGDP_PRJ)
C=0.5 (5/10, Siberian)
T=0.5 (5/10, Siberian)

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	25664	C=0.96579	T=0.03421
European	Sub	20494	C=0.96013	T=0.03987
African	Sub	2970	C=0.9956	T=0.0044
African Others	Sub	114	C=1.000	T=0.000
African American	Sub	2856	C=0.9954	T=0.0046
Asian	Sub	116	C=1.000	T=0.000
East Asian	Sub	88	C=1.00	T=0.00
Other Asian	Sub	28	C=1.00	T=0.00
Latin American 1	Sub	154	C=0.974	T=0.026
Latin American 2	Sub	616	C=0.981	T=0.019
South Asian	Sub	98	C=0.97	T=0.03
Other	Sub	1216	C=0.9762	T=0.0238

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	C=0.973550	T=0.026450
gnomAD - Genomes	Global	Study-wide	140264	C=0.971290	T=0.028710
gnomAD - Genomes	European	Sub	75946	C=0.95963	T=0.04037
gnomAD - Genomes	African	Sub	42042	C=0.99277	T=0.00723
gnomAD - Genomes	American	Sub	13668	C=0.97249	T=0.02751
gnomAD - Genomes	Ashkenazi Jewish	Sub	3322	C=0.9332	T=0.0668
gnomAD - Genomes	East Asian	Sub	3134	C=1.0000	T=0.0000
gnomAD - Genomes	Other	Sub	2152	C=0.9726	T=0.0274
Allele Frequency Aggregator	Total	Global	25570	C=0.96570	T=0.03430
Allele Frequency Aggregator	European	Sub	20418	C=0.95999	T=0.04001
Allele Frequency Aggregator	African	Sub	2970	C=0.9956	T=0.0044
Allele Frequency Aggregator	Other	Sub	1198	C=0.9766	T=0.0234
Allele Frequency Aggregator	Latin American 2	Sub	616	C=0.981	T=0.019
Allele Frequency Aggregator	Latin American 1	Sub	154	C=0.974	T=0.026
Allele Frequency Aggregator	Asian	Sub	116	C=1.000	T=0.000
Allele Frequency Aggregator	South Asian	Sub	98	C=0.97	T=0.03
1000Genomes_30x	Global	Study-wide	6404	C=0.9802	T=0.0198
1000Genomes_30x	African	Sub	1786	C=0.9989	T=0.0011
1000Genomes_30x	Europe	Sub	1266	C=0.9526	T=0.0474
1000Genomes_30x	South Asian	Sub	1202	C=0.9759	T=0.0241
1000Genomes_30x	East Asian	Sub	1170	C=1.0000	T=0.0000
1000Genomes_30x	American	Sub	980	C=0.963	T=0.037
1000Genomes	Global	Study-wide	5008	C=0.9804	T=0.0196
1000Genomes	African	Sub	1322	C=0.9992	T=0.0008
1000Genomes	East Asian	Sub	1008	C=0.9990	T=0.0010
1000Genomes	Europe	Sub	1006	C=0.9513	T=0.0487
1000Genomes	South Asian	Sub	978	C=0.976	T=0.024
1000Genomes	American	Sub	694	C=0.965	T=0.035
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9658	T=0.0342
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9639	T=0.0361
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9668	T=0.0332
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.950	T=0.050
Northern Sweden	ACPOP	Study-wide	600	C=0.980	T=0.020
Qatari	Global	Study-wide	216	C=0.972	T=0.028
The Danish reference pan genome	Danish	Study-wide	40	C=0.97	T=0.03
SGDP_PRJ	Global	Study-wide	18	C=0.50	T=0.50
Siberian	Global	Study-wide	10	C=0.5	T=0.5

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.929110C>T
GRCh37.p13 chr 1	NC_000001.10:g.864490C>T

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.610-1045… NM_001385640.1:c.610-1045C>T	N/A	Intron Variant
SAMD11 transcript variant 1	NM_001385641.1:c.610-1045… NM_001385641.1:c.610-1045C>T	N/A	Intron Variant
SAMD11 transcript variant 3	NM_152486.4:c.73-1045C>T	N/A	Intron Variant

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

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.929110=	NC_000001.11:g.929110C>T
GRCh37.p13 chr 1	NC_000001.10:g.864490=	NC_000001.10:g.864490C>T
SAMD11 transcript variant 2	NM_001385640.1:c.610-1045=	NM_001385640.1:c.610-1045C>T
SAMD11 transcript variant 1	NM_001385641.1:c.610-1045=	NM_001385641.1:c.610-1045C>T
SAMD11 transcript	NM_152486.2:c.73-1045=	NM_152486.2:c.73-1045C>T
SAMD11 transcript variant 3	NM_152486.4:c.73-1045=	NM_152486.4:c.73-1045C>T
SAMD11 transcript variant X1	XM_005244723.1:c.73-1045=	XM_005244723.1:c.73-1045C>T
SAMD11 transcript variant X2	XM_005244724.1:c.73-1045=	XM_005244724.1:c.73-1045C>T
SAMD11 transcript variant X3	XM_005244725.1:c.73-1045=	XM_005244725.1:c.73-1045C>T
SAMD11 transcript variant X4	XM_005244726.1:c.73-1045=	XM_005244726.1:c.73-1045C>T
SAMD11 transcript variant X5	XM_005244727.1:c.73-1045=	XM_005244727.1:c.73-1045C>T

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, 14 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HGSV	ss77544799	Dec 06, 2007 (129)
2	1000GENOMES	ss230395863	Jul 14, 2010 (132)
3	BL	ss252865290	May 09, 2011 (134)
4	ILLUMINA	ss533349713	Sep 08, 2015 (146)
5	EVA-GONL	ss974770189	Aug 21, 2014 (142)
6	1000GENOMES	ss1289342470	Aug 21, 2014 (142)
7	EVA_GENOME_DK	ss1573851411	Apr 01, 2015 (144)
8	EVA_DECODE	ss1584130094	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1599379377	Apr 01, 2015 (144)
10	EVA_UK10K_TWINSUK	ss1642373410	Apr 01, 2015 (144)
11	WEILL_CORNELL_DGM	ss1917961627	Feb 12, 2016 (147)
12	JJLAB	ss2019498827	Sep 14, 2016 (149)
13	USC_VALOUEV	ss2147485377	Dec 20, 2016 (150)
14	HUMAN_LONGEVITY	ss2159370597	Dec 20, 2016 (150)
15	GNOMAD	ss2750649219	Nov 08, 2017 (151)
16	AFFY	ss2984840997	Nov 08, 2017 (151)
17	AFFY	ss2985494988	Nov 08, 2017 (151)
18	SWEGEN	ss2986151068	Nov 08, 2017 (151)
19	CSHL	ss3343273238	Nov 08, 2017 (151)
20	ILLUMINA	ss3626006641	Oct 11, 2018 (152)
21	ILLUMINA	ss3653614747	Oct 11, 2018 (152)
22	EGCUT_WGS	ss3654262334	Jul 12, 2019 (153)
23	EVA_DECODE	ss3685993673	Jul 12, 2019 (153)
24	ACPOP	ss3726717038	Jul 12, 2019 (153)
25	SGDP_PRJ	ss3847998137	Apr 25, 2020 (154)
26	TOPMED	ss4436457685	Apr 25, 2021 (155)
27	1000G_HIGH_COVERAGE	ss5240866499	Oct 12, 2022 (156)
28	EVA	ss5316188308	Oct 12, 2022 (156)
29	HUGCELL_USP	ss5442114292	Oct 12, 2022 (156)
30	1000G_HIGH_COVERAGE	ss5512492299	Oct 12, 2022 (156)
31	SANFORD_IMAGENETICS	ss5624751485	Oct 12, 2022 (156)
32	EVA	ss5831419766	Oct 12, 2022 (156)
33	EVA	ss5906707239	Oct 12, 2022 (156)
34	EVA	ss5936584062	Oct 12, 2022 (156)
35	1000Genomes	NC_000001.10 - 864490	Oct 11, 2018 (152)
36	1000Genomes_30x	NC_000001.11 - 929110	Oct 12, 2022 (156)
37	The Avon Longitudinal Study of Parents and Children	NC_000001.10 - 864490	Oct 11, 2018 (152)
38	Genetic variation in the Estonian population	NC_000001.10 - 864490	Oct 11, 2018 (152)
39	The Danish reference pan genome	NC_000001.10 - 864490	Apr 25, 2020 (154)
40	gnomAD - Genomes	NC_000001.11 - 929110	Apr 25, 2021 (155)
41	Genome of the Netherlands Release 5	NC_000001.10 - 864490	Apr 25, 2020 (154)
42	Northern Sweden	NC_000001.10 - 864490	Jul 12, 2019 (153)
43	Qatari	NC_000001.10 - 864490	Apr 25, 2020 (154)
44	SGDP_PRJ	NC_000001.10 - 864490	Apr 25, 2020 (154)
45	Siberian	NC_000001.10 - 864490	Apr 25, 2020 (154)
46	TopMed	NC_000001.11 - 929110	Apr 25, 2021 (155)
47	UK 10K study - Twins	NC_000001.10 - 864490	Oct 11, 2018 (152)
48	ALFA	NC_000001.11 - 929110	Apr 25, 2021 (155)

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
ss77544799	NC_000001.8:904352:C:T	NC_000001.11:929109:C:T	(self)
ss252865290, ss1584130094	NC_000001.9:854352:C:T	NC_000001.11:929109:C:T	(self)
7331, 1452, 582, 1358645, 1106, 1903, 3557, 15117, 1731, 1452, ss230395863, ss533349713, ss974770189, ss1289342470, ss1573851411, ss1599379377, ss1642373410, ss1917961627, ss2019498827, ss2147485377, ss2750649219, ss2984840997, ss2985494988, ss2986151068, ss3343273238, ss3626006641, ss3653614747, ss3654262334, ss3726717038, ss3847998137, ss5316188308, ss5624751485, ss5831419766, ss5936584062	NC_000001.10:864489:C:T	NC_000001.11:929109:C:T	(self)
18234, 86858, 64020, 4217293198, ss2159370597, ss3685993673, ss4436457685, ss5240866499, ss5442114292, ss5512492299, ss5906707239	NC_000001.11:929109:C:T	NC_000001.11:929109:C:T	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs55678698

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs55678698