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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.


Current Build 155

Released April 9, 2021

Homo sapiens
chr2:69879166 (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.

T>A / T>C
Variation Type
SNV Single Nucleotide Variation
C=0.000007 (1/140270, GnomAD)
A=0.000 (0/330, HapMap)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GMCL1 : Non Coding Transcript Variant
0 citations
Genomic View
See rs on genome

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 2 NC_000002.12:g.69879166T>A
GRCh38.p13 chr 2 NC_000002.12:g.69879166T>C
GRCh37.p13 chr 2 NC_000002.11:g.70106298T>A
GRCh37.p13 chr 2 NC_000002.11:g.70106298T>C
Gene: GMCL1, germ cell-less 1, spermatogenesis associated (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GMCL1 transcript NM_178439.5:c.*162= N/A 3 Prime UTR Variant
GMCL1 transcript variant X3 XM_011533034.2:c.*162= N/A 3 Prime UTR Variant
GMCL1 transcript variant X5 XM_017004705.1:c.*162= N/A 3 Prime UTR Variant
GMCL1 transcript variant X1 XM_011533033.2:c.*162= N/A 3 Prime UTR Variant
GMCL1 transcript variant X4 XM_017004704.2:c.*162= N/A 3 Prime UTR Variant
GMCL1 transcript variant X2 XR_001738895.2:n.2046T>A N/A Non Coding Transcript Variant
GMCL1 transcript variant X2 XR_001738895.2:n.2046T>C N/A Non Coding Transcript 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

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").

Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Genomes Global Study-wide 140270 T=0.999993 C=0.000007
gnomAD - Genomes European Sub 75942 T=1.00000 C=0.00000
gnomAD - Genomes African Sub 42060 T=0.99998 C=0.00002
gnomAD - Genomes American Sub 13656 T=1.00000 C=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 T=1.0000 C=0.0000
gnomAD - Genomes East Asian Sub 3134 T=1.0000 C=0.0000
gnomAD - Genomes Other Sub 2154 T=1.0000 C=0.0000
HapMap Global Study-wide 330 T=1.000 A=0.000
HapMap African Sub 120 T=1.000 A=0.000
HapMap American Sub 120 T=1.000 A=0.000
HapMap Asian Sub 90 T=1.00 A=0.00

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= A C
GRCh38.p13 chr 2 NC_000002.12:g.69879166= NC_000002.12:g.69879166T>A NC_000002.12:g.69879166T>C
GRCh37.p13 chr 2 NC_000002.11:g.70106298= NC_000002.11:g.70106298T>A NC_000002.11:g.70106298T>C
GMCL1 transcript NM_178439.5:c.*162= NM_178439.5:c.*162T>A NM_178439.5:c.*162T>C
GMCL1 transcript NM_178439.4:c.*162= NM_178439.4:c.*162T>A NM_178439.4:c.*162T>C
GMCL1 transcript NM_178439.3:c.*162= NM_178439.3:c.*162T>A NM_178439.3:c.*162T>C
GMCL1 transcript variant X2 XR_001738895.2:n.2046= XR_001738895.2:n.2046T>A XR_001738895.2:n.2046T>C
GMCL1 transcript variant X1 XM_011533033.2:c.*162= XM_011533033.2:c.*162T>A XM_011533033.2:c.*162T>C
GMCL1 transcript variant X3 XM_011533034.2:c.*162= XM_011533034.2:c.*162T>A XM_011533034.2:c.*162T>C
GMCL1 transcript variant X4 XM_017004704.2:c.*162= XM_017004704.2:c.*162T>A XM_017004704.2:c.*162T>C
GMCL1 transcript variant X5 XM_017004705.1:c.*162= XM_017004705.1:c.*162T>A XM_017004705.1:c.*162T>C
FLJ13057 transcript NM_022471.1:c.*162= NM_022471.1:c.*162T>A NM_022471.1:c.*162T>C

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#.

35 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss6263511 Sep 28, 2016 (149)
2 ILLUMINA ss75301570 Dec 06, 2007 (129)
3 KRIBB_YJKIM ss119481298 Dec 01, 2009 (131)
4 ILLUMINA ss123187946 Dec 01, 2009 (131)
5 ILLUMINA ss154302763 Dec 01, 2009 (131)
6 ILLUMINA ss160691543 Dec 01, 2009 (131)
7 ILLUMINA ss171837737 Jul 04, 2010 (132)
8 ILLUMINA ss173762124 Jul 04, 2010 (132)
9 ILLUMINA ss480981667 May 04, 2012 (137)
10 ILLUMINA ss481002152 May 04, 2012 (137)
11 ILLUMINA ss481980338 Sep 08, 2015 (146)
12 ILLUMINA ss485285752 May 04, 2012 (137)
13 ILLUMINA ss537250161 Sep 08, 2015 (146)
14 ILLUMINA ss778342330 Sep 08, 2015 (146)
15 ILLUMINA ss783088778 Sep 08, 2015 (146)
16 ILLUMINA ss784046235 Sep 08, 2015 (146)
17 ILLUMINA ss825652754 Jul 19, 2016 (147)
18 ILLUMINA ss832347226 Sep 08, 2015 (146)
19 ILLUMINA ss833796940 Sep 08, 2015 (146)
20 ILLUMINA ss1752367216 Sep 08, 2015 (146)
21 ILLUMINA ss2633630484 Nov 08, 2017 (151)
22 ILLUMINA ss3628090819 Oct 11, 2018 (152)
23 ILLUMINA ss3631596464 Oct 11, 2018 (152)
24 ILLUMINA ss3633916587 Oct 11, 2018 (152)
25 ILLUMINA ss3634771822 Oct 11, 2018 (152)
26 ILLUMINA ss3635602760 Oct 11, 2018 (152)
27 ILLUMINA ss3636458930 Oct 11, 2018 (152)
28 ILLUMINA ss3637354640 Oct 11, 2018 (152)
29 ILLUMINA ss3638267178 Oct 11, 2018 (152)
30 ILLUMINA ss3640479124 Oct 11, 2018 (152)
31 ILLUMINA ss3643236640 Oct 11, 2018 (152)
32 ILLUMINA ss3745071735 Jul 13, 2019 (153)
33 ILLUMINA ss3772568529 Jul 13, 2019 (153)
34 EVA ss4017002503 Apr 26, 2021 (155)
35 GNOMAD ss4043476850 Apr 26, 2021 (155)
36 gnomAD - Genomes NC_000002.12 - 69879166 Apr 26, 2021 (155)
37 HapMap NC_000002.12 - 69879166 Apr 25, 2020 (154)

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
ss480981667, ss825652754, ss3643236640 NC_000002.10:69959801:T:A NC_000002.12:69879165:T:A (self)
ss481002152, ss481980338, ss485285752, ss537250161, ss778342330, ss783088778, ss784046235, ss832347226, ss833796940, ss1752367216, ss2633630484, ss3628090819, ss3631596464, ss3633916587, ss3634771822, ss3635602760, ss3636458930, ss3637354640, ss3638267178, ss3640479124, ss3745071735, ss3772568529, ss4017002503 NC_000002.11:70106297:T:A NC_000002.12:69879165:T:A (self)
1823509 NC_000002.12:69879165:T:A NC_000002.12:69879165:T:A (self)
ss6263511, ss75301570, ss119481298, ss123187946, ss154302763, ss160691543, ss171837737, ss173762124 NT_022184.15:48928184:T:A NC_000002.12:69879165:T:A (self)
61824902, ss4043476850 NC_000002.12:69879165:T:C NC_000002.12:69879165:T:C

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

No publications for rs4618082


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