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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.

rs116261102

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr1:17613168 (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
T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.000019 (5/264690, TOPMED)
C=0.000004 (1/250892, GnomAD_exome)
C=0.000029 (4/140152, GnomAD) (+ 5 more)
C=0.000017 (2/120218, ExAC)
C=0.00006 (1/16760, 8.3KJPN)
C=0.00000 (0/14050, ALFA)
C=0.00015 (2/13006, GO-ESP)
C=0.0002 (1/5008, 1000G)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ARHGEF10L : Synonymous 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.17613168T>C
GRCh37.p13 chr 1 NC_000001.10:g.17939663T>C
ARHGEF10L RefSeqGene NG_050860.1:g.97972T>C
Gene: ARHGEF10L, Rho guanine nucleotide exchange factor 10 like (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ARHGEF10L transcript variant 2 NM_001011722.2:c.610-2926…

NM_001011722.2:c.610-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant 3 NM_001319837.1:c.610-2926…

NM_001319837.1:c.610-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant 4 NM_001319838.1:c. N/A Genic Upstream Transcript Variant
ARHGEF10L transcript variant 5 NM_001328124.1:c. N/A Genic Upstream Transcript Variant
ARHGEF10L transcript variant 1 NM_018125.4:c.720T>C D [GAT] > D [GAC] Coding Sequence Variant
rho guanine nucleotide exchange factor 10-like protein isoform 1 NP_060595.3:p.Asp240= D (Asp) > D (Asp) Synonymous Variant
ARHGEF10L transcript variant 6 NR_137287.2:n.1019T>C N/A Non Coding Transcript Variant
ARHGEF10L transcript variant 7 NR_137288.2:n. N/A Intron Variant
ARHGEF10L transcript variant X2 XM_005245923.2:c.613-2926…

XM_005245923.2:c.613-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X9 XM_005245925.2:c.610-2926…

XM_005245925.2:c.610-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X1 XM_006710728.1:c.613-2926…

XM_006710728.1:c.613-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X7 XM_006710729.1:c.610-2926…

XM_006710729.1:c.610-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X6 XM_006710731.1:c.610-2926…

XM_006710731.1:c.610-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X8 XM_011541691.2:c.613-2926…

XM_011541691.2:c.613-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X10 XM_011541692.2:c.613-2926…

XM_011541692.2:c.613-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X11 XM_011541693.2:c.613-2926…

XM_011541693.2:c.613-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X12 XM_017001617.1:c.610-2926…

XM_017001617.1:c.610-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X16 XM_017001618.1:c.16-2926T…

XM_017001618.1:c.16-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X17 XM_017001619.1:c.613-2926…

XM_017001619.1:c.613-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X18 XM_017001620.1:c.613-2926…

XM_017001620.1:c.613-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X3 XM_024448059.1:c.613-2926…

XM_024448059.1:c.613-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X4 XM_024448061.1:c.613-2926…

XM_024448061.1:c.613-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X5 XM_024448062.1:c.613-2926…

XM_024448062.1:c.613-2926T>C

N/A Intron Variant
ARHGEF10L transcript variant X15 XM_005245929.3:c. N/A Genic Upstream Transcript Variant
ARHGEF10L transcript variant X26 XM_017001621.1:c.720T>C D [GAT] > D [GAC] Coding Sequence Variant
rho guanine nucleotide exchange factor 10-like protein isoform X12 XP_016857110.1:p.Asp240= D (Asp) > D (Asp) Synonymous Variant
ARHGEF10L transcript variant X27 XM_017001622.1:c.720T>C D [GAT] > D [GAC] Coding Sequence Variant
rho guanine nucleotide exchange factor 10-like protein isoform X13 XP_016857111.1:p.Asp240= D (Asp) > D (Asp) Synonymous Variant
ARHGEF10L transcript variant X14 XR_001737276.1:n. N/A Intron Variant
ARHGEF10L transcript variant X19 XR_001737277.1:n. N/A Intron Variant
ARHGEF10L transcript variant X23 XR_002956988.1:n. N/A Intron Variant
ARHGEF10L transcript variant X25 XR_002956989.1:n. N/A Intron Variant
ARHGEF10L transcript variant X13 XR_946686.3:n. N/A Intron Variant
ARHGEF10L transcript variant X20 XR_946688.2:n. N/A Intron Variant
ARHGEF10L transcript variant X21 XR_946689.2:n. N/A Intron Variant
ARHGEF10L transcript variant X22 XR_946690.2:n. N/A Intron Variant
ARHGEF10L transcript variant X24 XR_946691.2:n. 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

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 14050 T=1.00000 C=0.00000
European Sub 9690 T=1.0000 C=0.0000
African Sub 2898 T=1.0000 C=0.0000
African Others Sub 114 T=1.000 C=0.000
African American Sub 2784 T=1.0000 C=0.0000
Asian Sub 112 T=1.000 C=0.000
East Asian Sub 86 T=1.00 C=0.00
Other Asian Sub 26 T=1.00 C=0.00
Latin American 1 Sub 146 T=1.000 C=0.000
Latin American 2 Sub 610 T=1.000 C=0.000
South Asian Sub 98 T=1.00 C=0.00
Other Sub 496 T=1.000 C=0.000


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 T=0.999981 C=0.000019
gnomAD - Exomes Global Study-wide 250892 T=0.999996 C=0.000004
gnomAD - Exomes European Sub 135252 T=0.999993 C=0.000007
gnomAD - Exomes Asian Sub 48842 T=1.00000 C=0.00000
gnomAD - Exomes American Sub 34392 T=1.00000 C=0.00000
gnomAD - Exomes African Sub 16252 T=1.00000 C=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 10044 T=1.00000 C=0.00000
gnomAD - Exomes Other Sub 6110 T=1.0000 C=0.0000
gnomAD - Genomes Global Study-wide 140152 T=0.999971 C=0.000029
gnomAD - Genomes European Sub 75908 T=0.99999 C=0.00001
gnomAD - Genomes African Sub 42000 T=0.99995 C=0.00005
gnomAD - Genomes American Sub 13650 T=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3320 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3126 T=0.9997 C=0.0003
gnomAD - Genomes Other Sub 2148 T=1.0000 C=0.0000
ExAC Global Study-wide 120218 T=0.999983 C=0.000017
ExAC Europe Sub 73020 T=0.99999 C=0.00001
ExAC Asian Sub 24330 T=1.00000 C=0.00000
ExAC American Sub 11574 T=1.00000 C=0.00000
ExAC African Sub 10392 T=0.99990 C=0.00010
ExAC Other Sub 902 T=1.000 C=0.000
8.3KJPN JAPANESE Study-wide 16760 T=0.99994 C=0.00006
Allele Frequency Aggregator Total Global 14050 T=1.00000 C=0.00000
Allele Frequency Aggregator European Sub 9690 T=1.0000 C=0.0000
Allele Frequency Aggregator African Sub 2898 T=1.0000 C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 T=1.000 C=0.000
Allele Frequency Aggregator Other Sub 496 T=1.000 C=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 T=1.000 C=0.000
Allele Frequency Aggregator Asian Sub 112 T=1.000 C=0.000
Allele Frequency Aggregator South Asian Sub 98 T=1.00 C=0.00
GO Exome Sequencing Project Global Study-wide 13006 T=0.99985 C=0.00015
GO Exome Sequencing Project European American Sub 8600 T=1.0000 C=0.0000
GO Exome Sequencing Project African American Sub 4406 T=0.9995 C=0.0005
1000Genomes Global Study-wide 5008 T=0.9998 C=0.0002
1000Genomes African Sub 1322 T=0.9992 C=0.0008
1000Genomes East Asian Sub 1008 T=1.0000 C=0.0000
1000Genomes Europe Sub 1006 T=1.0000 C=0.0000
1000Genomes South Asian Sub 978 T=1.000 C=0.000
1000Genomes American Sub 694 T=1.000 C=0.000
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 T= C
GRCh38.p13 chr 1 NC_000001.11:g.17613168= NC_000001.11:g.17613168T>C
GRCh37.p13 chr 1 NC_000001.10:g.17939663= NC_000001.10:g.17939663T>C
ARHGEF10L RefSeqGene NG_050860.1:g.97972= NG_050860.1:g.97972T>C
ARHGEF10L transcript variant 1 NM_018125.4:c.720= NM_018125.4:c.720T>C
ARHGEF10L transcript variant 1 NM_018125.3:c.720= NM_018125.3:c.720T>C
ARHGEF10L transcript variant 6 NR_137287.2:n.1019= NR_137287.2:n.1019T>C
ARHGEF10L transcript variant 6 NR_137287.1:n.882= NR_137287.1:n.882T>C
ARHGEF10L transcript variant X26 XM_017001621.1:c.720= XM_017001621.1:c.720T>C
ARHGEF10L transcript variant X27 XM_017001622.1:c.720= XM_017001622.1:c.720T>C
rho guanine nucleotide exchange factor 10-like protein isoform 1 NP_060595.3:p.Asp240= NP_060595.3:p.Asp240=
rho guanine nucleotide exchange factor 10-like protein isoform X12 XP_016857110.1:p.Asp240= XP_016857110.1:p.Asp240=
rho guanine nucleotide exchange factor 10-like protein isoform X13 XP_016857111.1:p.Asp240= XP_016857111.1:p.Asp240=
ARHGEF10L transcript variant 2 NM_001011722.2:c.610-2926= NM_001011722.2:c.610-2926T>C
ARHGEF10L transcript variant 3 NM_001319837.1:c.610-2926= NM_001319837.1:c.610-2926T>C
ARHGEF10L transcript variant X3 XM_005245923.1:c.613-2926= XM_005245923.1:c.613-2926T>C
ARHGEF10L transcript variant X2 XM_005245923.2:c.613-2926= XM_005245923.2:c.613-2926T>C
ARHGEF10L transcript variant X4 XM_005245924.1:c.613-2926= XM_005245924.1:c.613-2926T>C
ARHGEF10L transcript variant X5 XM_005245925.1:c.610-2926= XM_005245925.1:c.610-2926T>C
ARHGEF10L transcript variant X9 XM_005245925.2:c.610-2926= XM_005245925.2:c.610-2926T>C
ARHGEF10L transcript variant X6 XM_005245926.1:c.610-2926= XM_005245926.1:c.610-2926T>C
ARHGEF10L transcript variant X8 XM_005245928.1:c.43-2926= XM_005245928.1:c.43-2926T>C
ARHGEF10L transcript variant X1 XM_006710728.1:c.613-2926= XM_006710728.1:c.613-2926T>C
ARHGEF10L transcript variant X7 XM_006710729.1:c.610-2926= XM_006710729.1:c.610-2926T>C
ARHGEF10L transcript variant X6 XM_006710731.1:c.610-2926= XM_006710731.1:c.610-2926T>C
ARHGEF10L transcript variant X8 XM_011541691.2:c.613-2926= XM_011541691.2:c.613-2926T>C
ARHGEF10L transcript variant X10 XM_011541692.2:c.613-2926= XM_011541692.2:c.613-2926T>C
ARHGEF10L transcript variant X11 XM_011541693.2:c.613-2926= XM_011541693.2:c.613-2926T>C
ARHGEF10L transcript variant X12 XM_017001617.1:c.610-2926= XM_017001617.1:c.610-2926T>C
ARHGEF10L transcript variant X16 XM_017001618.1:c.16-2926= XM_017001618.1:c.16-2926T>C
ARHGEF10L transcript variant X17 XM_017001619.1:c.613-2926= XM_017001619.1:c.613-2926T>C
ARHGEF10L transcript variant X18 XM_017001620.1:c.613-2926= XM_017001620.1:c.613-2926T>C
ARHGEF10L transcript variant X3 XM_024448059.1:c.613-2926= XM_024448059.1:c.613-2926T>C
ARHGEF10L transcript variant X4 XM_024448061.1:c.613-2926= XM_024448061.1:c.613-2926T>C
ARHGEF10L transcript variant X5 XM_024448062.1:c.613-2926= XM_024448062.1:c.613-2926T>C
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#.

15 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss217411014 Jul 14, 2010 (132)
2 1000GENOMES ss488654920 May 04, 2012 (137)
3 NHLBI-ESP ss712280413 Apr 25, 2013 (138)
4 1000GENOMES ss1289865737 Aug 21, 2014 (142)
5 EVA_EXAC ss1685350622 Apr 01, 2015 (144)
6 HUMAN_LONGEVITY ss2160378745 Dec 20, 2016 (150)
7 TOPMED ss2322559511 Dec 20, 2016 (150)
8 GNOMAD ss2731191738 Nov 08, 2017 (151)
9 GNOMAD ss2746239722 Nov 08, 2017 (151)
10 GNOMAD ss2752192106 Nov 08, 2017 (151)
11 TOPMED ss3069847231 Nov 08, 2017 (151)
12 EVA ss3745885634 Jul 12, 2019 (153)
13 EVA ss3823569010 Apr 25, 2020 (154)
14 TOPMED ss4440704549 Apr 27, 2021 (155)
15 TOMMO_GENOMICS ss5142731587 Apr 27, 2021 (155)
16 1000Genomes NC_000001.10 - 17939663 Oct 11, 2018 (152)
17 ExAC NC_000001.10 - 17939663 Oct 11, 2018 (152)
18 gnomAD - Genomes NC_000001.11 - 17613168 Apr 27, 2021 (155)
19 gnomAD - Exomes NC_000001.10 - 17939663 Jul 12, 2019 (153)
20 GO Exome Sequencing Project NC_000001.10 - 17939663 Oct 11, 2018 (152)
21 8.3KJPN NC_000001.10 - 17939663 Apr 27, 2021 (155)
22 TopMed NC_000001.11 - 17613168 Apr 27, 2021 (155)
23 ALFA NC_000001.11 - 17613168 Apr 27, 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
ss217411014 NC_000001.9:17812249:T:C NC_000001.11:17613167:T:C (self)
548199, 4533187, 204302, 27728, 700894, ss488654920, ss712280413, ss1289865737, ss1685350622, ss2322559511, ss2731191738, ss2746239722, ss2752192106, ss3745885634, ss3823569010, ss5142731587 NC_000001.10:17939662:T:C NC_000001.11:17613167:T:C (self)
3840453, 2706189, 4310884, 1547578278, ss2160378745, ss3069847231, ss4440704549 NC_000001.11:17613167:T:C NC_000001.11:17613167:T:C (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 rs116261102

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