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dbSNP Short Genetic Variations

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.

rs10504576

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr8:74354444 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.46509 (58400/125568, TOPMED)
G=0.4706 (14536/30886, GnomAD)
G=0.452 (2264/5008, 1000G) (+ 4 more)
A=0.500 (2240/4480, Estonian)
G=0.500 (2240/4480, Estonian)
G=0.492 (1895/3854, ALSPAC)
G=0.471 (1748/3708, TWINSUK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GDAP1 : Intron Variant
Publications
1 citation
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 8 NC_000008.11:g.74354444A>G
GRCh37.p13 chr 8 NC_000008.10:g.75266679A>G
GDAP1 RefSeqGene (LRG_244) NG_008787.3:g.38315A>G
Gene: GDAP1, ganglioside induced differentiation associated protein 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GDAP1 transcript variant 2 NM_001040875.2:c. N/A Intron Variant
GDAP1 transcript variant 1 NM_018972.2:c. N/A Intron Variant
GDAP1 transcript variant 3 NR_046346.1:n. N/A Intron Variant
GDAP1 transcript variant X1 XM_011517551.3:c. N/A Intron Variant
GDAP1 transcript variant X4 XM_011517552.3:c. N/A Intron Variant
GDAP1 transcript variant X2 XM_017013585.2:c. N/A Intron Variant
GDAP1 transcript variant X3 XM_017013586.2: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
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").

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Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 A=0.53491 G=0.46509
gnomAD - Genomes Global Study-wide 30886 A=0.5294 G=0.4706
gnomAD - Genomes European Sub 18440 A=0.5081 G=0.4919
gnomAD - Genomes African Sub 8722 A=0.550 G=0.450
gnomAD - Genomes East Asian Sub 1612 A=0.607 G=0.393
gnomAD - Genomes Other Sub 974 A=0.55 G=0.45
gnomAD - Genomes American Sub 836 A=0.61 G=0.39
gnomAD - Genomes Ashkenazi Jewish Sub 302 A=0.50 G=0.50
1000Genomes Global Study-wide 5008 A=0.548 G=0.452
1000Genomes African Sub 1322 A=0.557 G=0.443
1000Genomes East Asian Sub 1008 A=0.579 G=0.421
1000Genomes Europe Sub 1006 A=0.547 G=0.453
1000Genomes South Asian Sub 978 A=0.45 G=0.55
1000Genomes American Sub 694 A=0.62 G=0.38
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.500 G=0.500
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.508 G=0.492
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.529 G=0.471
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 A= G Note
GRCh38.p12 chr 8 NC_000008.11:g.74354444A= NC_000008.11:g.74354444A>G
GRCh37.p13 chr 8 NC_000008.10:g.75266679A= NC_000008.10:g.75266679A>G
GDAP1 RefSeqGene (LRG_244) NG_008787.3:g.38315A= NG_008787.3:g.38315A>G
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#.

71 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss14898787 Dec 05, 2003 (119)
2 SSAHASNP ss22763027 Apr 05, 2004 (121)
3 PERLEGEN ss23551976 Sep 20, 2004 (123)
4 AFFY ss65973573 Dec 01, 2006 (127)
5 ILLUMINA ss66824978 Dec 01, 2006 (127)
6 ILLUMINA ss66890790 Dec 01, 2006 (127)
7 ILLUMINA ss66994212 Dec 01, 2006 (127)
8 ILLUMINA ss70371982 May 17, 2007 (127)
9 ILLUMINA ss70486730 May 24, 2008 (130)
10 ILLUMINA ss71010965 May 17, 2007 (127)
11 ILLUMINA ss75916448 Dec 07, 2007 (129)
12 HGSV ss79039031 Dec 07, 2007 (129)
13 KRIBB_YJKIM ss84963794 Dec 14, 2007 (130)
14 HGSV ss85674671 Dec 14, 2007 (130)
15 BCMHGSC_JDW ss93911009 Mar 25, 2008 (129)
16 HUMANGENOME_JCVI ss97881802 Feb 04, 2009 (130)
17 1000GENOMES ss108132255 Jan 23, 2009 (130)
18 ILLUMINA-UK ss116016195 Feb 14, 2009 (130)
19 ILLUMINA ss121342719 Dec 01, 2009 (131)
20 ENSEMBL ss134335673 Dec 01, 2009 (131)
21 ENSEMBL ss143566607 Dec 01, 2009 (131)
22 ILLUMINA ss152767006 Dec 01, 2009 (131)
23 GMI ss156520832 Dec 01, 2009 (131)
24 ILLUMINA ss159131647 Dec 01, 2009 (131)
25 COMPLETE_GENOMICS ss166775127 Jul 04, 2010 (132)
26 ILLUMINA ss169488948 Jul 04, 2010 (132)
27 ILLUMINA ss170261997 Jul 04, 2010 (132)
28 BUSHMAN ss199339415 Jul 04, 2010 (132)
29 BCM-HGSC-SUB ss208508509 Jul 04, 2010 (132)
30 1000GENOMES ss210569921 Jul 14, 2010 (132)
31 1000GENOMES ss223783883 Jul 14, 2010 (132)
32 1000GENOMES ss234492225 Jul 15, 2010 (132)
33 1000GENOMES ss241337238 Jul 15, 2010 (132)
34 GMI ss279867169 May 04, 2012 (137)
35 GMI ss285867660 Apr 25, 2013 (138)
36 PJP ss294107702 May 09, 2011 (134)
37 ILLUMINA ss536617092 Sep 08, 2015 (146)
38 TISHKOFF ss560840794 Apr 25, 2013 (138)
39 SSMP ss655277261 Apr 25, 2013 (138)
40 ILLUMINA ss825341593 Apr 01, 2015 (144)
41 ILLUMINA ss832644332 Aug 21, 2014 (142)
42 ILLUMINA ss833235021 Aug 21, 2014 (142)
43 EVA-GONL ss985671929 Aug 21, 2014 (142)
44 JMKIDD_LAB ss1075635536 Aug 21, 2014 (142)
45 1000GENOMES ss1330456357 Aug 21, 2014 (142)
46 DDI ss1431559345 Apr 01, 2015 (144)
47 EVA_GENOME_DK ss1582741784 Apr 01, 2015 (144)
48 EVA_DECODE ss1595272656 Apr 01, 2015 (144)
49 EVA_UK10K_ALSPAC ss1620956042 Apr 01, 2015 (144)
50 EVA_UK10K_TWINSUK ss1663950075 Apr 01, 2015 (144)
51 EVA_SVP ss1713046481 Apr 01, 2015 (144)
52 HAMMER_LAB ss1805600264 Sep 08, 2015 (146)
53 WEILL_CORNELL_DGM ss1928956750 Feb 12, 2016 (147)
54 GENOMED ss1971012257 Jul 19, 2016 (147)
55 JJLAB ss2025181249 Sep 14, 2016 (149)
56 USC_VALOUEV ss2153406880 Dec 20, 2016 (150)
57 HUMAN_LONGEVITY ss2304353612 Dec 20, 2016 (150)
58 TOPMED ss2474215023 Dec 20, 2016 (150)
59 SYSTEMSBIOZJU ss2627068657 Nov 08, 2017 (151)
60 GRF ss2709180491 Nov 08, 2017 (151)
61 GNOMAD ss2868493580 Nov 08, 2017 (151)
62 SWEGEN ss3003418914 Nov 08, 2017 (151)
63 BIOINF_KMB_FNS_UNIBA ss3026376538 Nov 08, 2017 (151)
64 CSHL ss3348247512 Nov 08, 2017 (151)
65 TOPMED ss3566123775 Nov 08, 2017 (151)
66 ILLUMINA ss3630088724 Oct 12, 2018 (152)
67 ILLUMINA ss3638767814 Oct 12, 2018 (152)
68 ILLUMINA ss3639386350 Oct 12, 2018 (152)
69 ILLUMINA ss3639722828 Oct 12, 2018 (152)
70 ILLUMINA ss3643698177 Oct 12, 2018 (152)
71 URBANLAB ss3648944099 Oct 12, 2018 (152)
72 1000Genomes NC_000008.10 - 75266679 Oct 12, 2018 (152)
73 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 75266679 Oct 12, 2018 (152)
74 Genetic variation in the Estonian population NC_000008.10 - 75266679 Oct 12, 2018 (152)
75 gnomAD - Genomes NC_000008.10 - 75266679 Oct 12, 2018 (152)
76 TopMed NC_000008.11 - 74354444 Oct 12, 2018 (152)
77 UK 10K study - Twins NC_000008.10 - 75266679 Oct 12, 2018 (152)
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)
rs57840789 May 24, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss79039031, ss85674671, ss93911009, ss108132255, ss116016195, ss166775127, ss199339415, ss208508509, ss210569921, ss279867169, ss285867660, ss294107702, ss825341593, ss1595272656, ss1713046481, ss3639386350, ss3639722828, ss3643698177 NC_000008.9:75429233:A:G NC_000008.11:74354443:A:G (self)
42601486, 23694504, 16848034, 209121334, 23694504, ss223783883, ss234492225, ss241337238, ss536617092, ss560840794, ss655277261, ss832644332, ss833235021, ss985671929, ss1075635536, ss1330456357, ss1431559345, ss1582741784, ss1620956042, ss1663950075, ss1805600264, ss1928956750, ss1971012257, ss2025181249, ss2153406880, ss2474215023, ss2627068657, ss2709180491, ss2868493580, ss3003418914, ss3348247512, ss3630088724, ss3638767814 NC_000008.10:75266678:A:G NC_000008.11:74354443:A:G (self)
392872630, ss2304353612, ss3026376538, ss3566123775, ss3648944099 NC_000008.11:74354443:A:G NC_000008.11:74354443:A:G (self)
ss22763027 NT_008183.17:27109228:A:G NC_000008.11:74354443:A:G (self)
ss14898787, ss23551976, ss65973573, ss66824978, ss66890790, ss66994212, ss70371982, ss70486730, ss71010965, ss75916448, ss84963794, ss97881802, ss121342719, ss134335673, ss143566607, ss152767006, ss156520832, ss159131647, ss169488948, ss170261997 NT_008183.19:27131079:A:G NC_000008.11:74354443:A:G (self)
Help

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

1 citation for rs10504576
PMID Title Author Year Journal
17903300 Genome-wide association to body mass index and waist circumference: the Framingham Heart Study 100K project. Fox CS et al. 2007 BMC medical genetics

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.post104+4a6ee9c