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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 Aliases 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.

rs1755609

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr9:6641917 (GRCh38.p12) 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
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.307411 (38601/125568, TOPMED)
A=0.27904 (8748/31350, GnomAD)
A=0.3594 (1800/5008, 1000G) (+ 5 more)
A=0.1719 (770/4480, Estonian)
A=0.2169 (836/3854, ALSPAC)
A=0.2263 (839/3708, TWINSUK)
A=0.253 (152/600, NorthernSweden)
A=0.486 (104/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GLDC : Intron 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.p12 chr 9 NC_000009.12:g.6641917G>A
GRCh37.p13 chr 9 NC_000009.11:g.6641917G>A
GLDC RefSeqGene (LRG_643) NG_016397.1:g.8776C>T
Gene: GLDC, glycine decarboxylase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GLDC transcript NM_000170.2:c. 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 (New)
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: 20200227123210
Population Group Sample Size Ref Allele Alt Allele
Total Global 8990 G=0.7115 A=0.2885
European Sub 5184 G=0.7620 A=0.2380
African Sub 760 G=0.639 A=0.361
African Others Sub 18 G=0.50 A=0.50
African American Sub 742 G=0.643 A=0.357
Asian Sub 52 G=0.29 A=0.71
East Asian Sub 18 G=0.28 A=0.72
Other Asian Sub 34 G=0.29 A=0.71
Latin American 1 Sub 146 G=0.712 A=0.288
Latin American 2 Sub 2152 G=0.6371 A=0.3629
South Asian Sub 16 G=0.75 A=0.25
Other Sub 680 G=0.674 A=0.326


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 125568 G=0.692589 A=0.307411
gnomAD - Genomes Global Study-wide 31350 G=0.72096 A=0.27904
gnomAD - Genomes European Sub 18878 G=0.78531 A=0.21469
gnomAD - Genomes African Sub 8694 G=0.6268 A=0.3732
gnomAD - Genomes East Asian Sub 1556 G=0.4942 A=0.5058
gnomAD - Genomes Other Sub 1086 G=0.7357 A=0.2643
gnomAD - Genomes American Sub 846 G=0.647 A=0.353
gnomAD - Genomes Ashkenazi Jewish Sub 290 G=0.734 A=0.266
1000Genomes Global Study-wide 5008 G=0.6406 A=0.3594
1000Genomes African Sub 1322 G=0.6120 A=0.3880
1000Genomes East Asian Sub 1008 G=0.4861 A=0.5139
1000Genomes Europe Sub 1006 G=0.7634 A=0.2366
1000Genomes South Asian Sub 978 G=0.729 A=0.271
1000Genomes American Sub 694 G=0.617 A=0.383
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.8281 A=0.1719
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.7831 A=0.2169
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.7737 A=0.2263
Northern Sweden ACPOP Study-wide 600 G=0.747 A=0.253
A Vietnamese Genetic Variation Database Global Study-wide 214 G=0.514 A=0.486
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 Note
GRCh38.p12 chr 9 NC_000009.12:g.6641917= NC_000009.12:g.6641917G>A
GRCh37.p13 chr 9 NC_000009.11:g.6641917= NC_000009.11:g.6641917G>A
GLDC RefSeqGene (LRG_643) NG_016397.1:g.8776= NG_016397.1:g.8776C>T
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#.

55 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss2606851 Nov 09, 2000 (89)
2 WI_SSAHASNP ss12002849 Jul 11, 2003 (116)
3 SSAHASNP ss22808965 Apr 05, 2004 (123)
4 ABI ss43891384 Mar 14, 2006 (126)
5 AFFY ss66438994 Nov 29, 2006 (127)
6 AFFY ss76218776 Dec 08, 2007 (130)
7 KRIBB_YJKIM ss81578831 Dec 15, 2007 (130)
8 BCMHGSC_JDW ss94002487 Mar 25, 2008 (129)
9 HUMANGENOME_JCVI ss97773945 Feb 06, 2009 (130)
10 BGI ss104593055 Dec 01, 2009 (131)
11 1000GENOMES ss108554862 Jan 23, 2009 (130)
12 1000GENOMES ss114079674 Jan 25, 2009 (130)
13 ILLUMINA-UK ss115681350 Feb 14, 2009 (130)
14 ENSEMBL ss133614705 Dec 01, 2009 (131)
15 ENSEMBL ss143916354 Dec 01, 2009 (131)
16 GMI ss157130090 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss164401265 Jul 04, 2010 (132)
18 AFFY ss172854504 Jul 04, 2010 (132)
19 1000GENOMES ss224097910 Jul 14, 2010 (132)
20 1000GENOMES ss234708074 Jul 15, 2010 (132)
21 1000GENOMES ss241505448 Jul 15, 2010 (132)
22 BL ss254017232 May 09, 2011 (134)
23 GMI ss280087283 May 04, 2012 (137)
24 PJP ss294320175 May 09, 2011 (134)
25 TISHKOFF ss561209324 Apr 25, 2013 (138)
26 SSMP ss655637696 Apr 25, 2013 (138)
27 EVA-GONL ss986265589 Aug 21, 2014 (142)
28 JMKIDD_LAB ss1076075218 Aug 21, 2014 (142)
29 1000GENOMES ss1332728135 Aug 21, 2014 (142)
30 DDI ss1431736160 Apr 01, 2015 (144)
31 EVA_GENOME_DK ss1582967918 Apr 01, 2015 (144)
32 EVA_DECODE ss1595891231 Apr 01, 2015 (144)
33 EVA_UK10K_ALSPAC ss1622162030 Apr 01, 2015 (144)
34 EVA_UK10K_TWINSUK ss1665156063 Apr 01, 2015 (144)
35 EVA_SVP ss1713087311 Apr 01, 2015 (144)
36 HAMMER_LAB ss1805859271 Sep 08, 2015 (146)
37 WEILL_CORNELL_DGM ss1929545310 Feb 12, 2016 (147)
38 GENOMED ss1971143905 Jul 19, 2016 (147)
39 JJLAB ss2025479811 Sep 14, 2016 (149)
40 USC_VALOUEV ss2153709756 Dec 20, 2016 (150)
41 HUMAN_LONGEVITY ss2309042517 Dec 20, 2016 (150)
42 TOPMED ss2479050141 Dec 20, 2016 (150)
43 SYSTEMSBIOZJU ss2627215855 Nov 08, 2017 (151)
44 GRF ss2709506592 Nov 08, 2017 (151)
45 GNOMAD ss2874951404 Nov 08, 2017 (151)
46 SWEGEN ss3004318627 Nov 08, 2017 (151)
47 BIOINF_KMB_FNS_UNIBA ss3026528103 Nov 08, 2017 (151)
48 CSHL ss3348502544 Nov 08, 2017 (151)
49 TOPMED ss3580928973 Nov 08, 2017 (151)
50 URBANLAB ss3649060737 Oct 12, 2018 (152)
51 EGCUT_WGS ss3672050884 Jul 13, 2019 (153)
52 EVA_DECODE ss3723394486 Jul 13, 2019 (153)
53 ACPOP ss3736272079 Jul 13, 2019 (153)
54 EVA ss3768861478 Jul 13, 2019 (153)
55 KHV_HUMAN_GENOMES ss3812021018 Jul 13, 2019 (153)
56 1000Genomes NC_000009.11 - 6641917 Oct 12, 2018 (152)
57 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 6641917 Oct 12, 2018 (152)
58 Genetic variation in the Estonian population NC_000009.11 - 6641917 Oct 12, 2018 (152)
59 gnomAD - Genomes NC_000009.11 - 6641917 Jul 13, 2019 (153)
60 Northern Sweden NC_000009.11 - 6641917 Jul 13, 2019 (153)
61 TopMed NC_000009.12 - 6641917 Oct 12, 2018 (152)
62 UK 10K study - Twins NC_000009.11 - 6641917 Oct 12, 2018 (152)
63 A Vietnamese Genetic Variation Database NC_000009.11 - 6641917 Jul 13, 2019 (153)
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)
rs13288141 Sep 24, 2004 (123)
rs56572658 May 27, 2008 (130)
rs59594563 Feb 27, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss66438994, ss76218776, ss94002487, ss108554862, ss114079674, ss115681350, ss164401265, ss172854504, ss254017232, ss280087283, ss294320175, ss1595891231, ss1713087311 NC_000009.10:6631916:G:A NC_000009.12:6641916:G:A (self)
44951470, 25012686, 17789132, 122856020, 9556944, 25012686, 5552443, ss224097910, ss234708074, ss241505448, ss561209324, ss655637696, ss986265589, ss1076075218, ss1332728135, ss1431736160, ss1582967918, ss1622162030, ss1665156063, ss1805859271, ss1929545310, ss1971143905, ss2025479811, ss2153709756, ss2479050141, ss2627215855, ss2709506592, ss2874951404, ss3004318627, ss3348502544, ss3672050884, ss3736272079, ss3768861478 NC_000009.11:6641916:G:A NC_000009.12:6641916:G:A (self)
405043395, ss2309042517, ss3026528103, ss3580928973, ss3649060737, ss3723394486, ss3812021018 NC_000009.12:6641916:G:A NC_000009.12:6641916:G:A (self)
ss12002849 NT_008413.15:6631916:G:A NC_000009.12:6641916:G:A (self)
ss22808965 NT_008413.16:6631916:G:A NC_000009.12:6641916:G:A (self)
ss2606851, ss43891384, ss81578831, ss97773945, ss104593055, ss133614705, ss143916354, ss157130090 NT_008413.18:6631916:G:A NC_000009.12:6641916:G:A (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 rs1755609

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.post411+8fd821c