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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.

rs6996971

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr8:74380257 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.49259 (61853/125568, TOPMED)
C=0.4883 (15085/30890, GnomAD)
T=0.494 (2474/5008, 1000G) (+ 3 more)
T=0.499 (2234/4480, Estonian)
T=0.491 (1892/3854, ALSPAC)
T=0.472 (1751/3708, 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.74380257C>T
GRCh37.p13 chr 8 NC_000008.10:g.75292492C>T
GDAP1 RefSeqGene (LRG_244) NG_008787.3:g.64128C>T
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 Genic Downstream Transcript Variant
GDAP1 transcript variant 1 NM_018972.2:c. N/A Genic Downstream Transcript Variant
GDAP1 transcript variant 3 NR_046346.1:n. N/A Genic Downstream Transcript Variant
GDAP1 transcript variant X2 XM_017013585.2:c. N/A Intron Variant
GDAP1 transcript variant X1 XM_011517551.3:c. N/A Genic Downstream Transcript Variant
GDAP1 transcript variant X4 XM_011517552.3:c. N/A Genic Downstream Transcript Variant
GDAP1 transcript variant X3 XM_017013586.2:c. N/A Genic Downstream Transcript 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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 C=0.49259 T=0.50741
gnomAD - Genomes Global Study-wide 30890 C=0.4883 T=0.5117
gnomAD - Genomes European Sub 18456 C=0.5083 T=0.4917
gnomAD - Genomes African Sub 8702 C=0.406 T=0.594
gnomAD - Genomes East Asian Sub 1610 C=0.605 T=0.395
gnomAD - Genomes Other Sub 982 C=0.55 T=0.45
gnomAD - Genomes American Sub 838 C=0.61 T=0.39
gnomAD - Genomes Ashkenazi Jewish Sub 302 C=0.51 T=0.49
1000Genomes Global Study-wide 5008 C=0.506 T=0.494
1000Genomes African Sub 1322 C=0.402 T=0.598
1000Genomes East Asian Sub 1008 C=0.580 T=0.420
1000Genomes Europe Sub 1006 C=0.544 T=0.456
1000Genomes South Asian Sub 978 C=0.47 T=0.53
1000Genomes American Sub 694 C=0.60 T=0.40
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.501 T=0.499
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.509 T=0.491
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.528 T=0.472
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 C= T Note
GRCh38.p12 chr 8 NC_000008.11:g.74380257C= NC_000008.11:g.74380257C>T
GRCh37.p13 chr 8 NC_000008.10:g.75292492C= NC_000008.10:g.75292492C>T
GDAP1 RefSeqGene (LRG_244) NG_008787.3:g.64128C= NG_008787.3:g.64128C>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#.

102 SubSNP, 6 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10450739 Jul 11, 2003 (116)
2 PERLEGEN ss14898793 Dec 05, 2003 (119)
3 SC_SNP ss15690774 Feb 27, 2004 (120)
4 CSHL-HAPMAP ss20340668 Feb 27, 2004 (120)
5 SSAHASNP ss22743694 Apr 05, 2004 (121)
6 PERLEGEN ss24528756 Sep 20, 2004 (123)
7 ABI ss44923642 Mar 15, 2006 (126)
8 AFFY ss65973560 Nov 30, 2006 (127)
9 ILLUMINA ss66848859 Nov 30, 2006 (127)
10 ILLUMINA ss67527137 Nov 30, 2006 (127)
11 ILLUMINA ss67895323 Nov 30, 2006 (127)
12 ILLUMINA ss70901163 May 25, 2008 (130)
13 ILLUMINA ss71496519 May 17, 2007 (127)
14 ILLUMINA ss75873418 Dec 06, 2007 (129)
15 AFFY ss76420479 Dec 06, 2007 (129)
16 HGSV ss77150209 Dec 06, 2007 (129)
17 ILLUMINA ss79241716 Dec 15, 2007 (130)
18 KRIBB_YJKIM ss84593456 Dec 15, 2007 (130)
19 BCMHGSC_JDW ss93911054 Mar 25, 2008 (129)
20 HUMANGENOME_JCVI ss97881833 Feb 05, 2009 (130)
21 1000GENOMES ss108132447 Jan 23, 2009 (130)
22 1000GENOMES ss113231370 Jan 25, 2009 (130)
23 ILLUMINA-UK ss116016311 Feb 14, 2009 (130)
24 ILLUMINA ss122665393 Dec 01, 2009 (131)
25 ENSEMBL ss134335562 Dec 01, 2009 (131)
26 ENSEMBL ss143566785 Dec 01, 2009 (131)
27 ILLUMINA ss154397353 Dec 01, 2009 (131)
28 GMI ss156521187 Dec 01, 2009 (131)
29 ILLUMINA ss159572767 Dec 01, 2009 (131)
30 ILLUMINA ss160835003 Dec 01, 2009 (131)
31 COMPLETE_GENOMICS ss165011590 Jul 04, 2010 (132)
32 COMPLETE_GENOMICS ss166775432 Jul 04, 2010 (132)
33 ILLUMINA ss172230102 Jul 04, 2010 (132)
34 ILLUMINA ss174198601 Jul 04, 2010 (132)
35 BUSHMAN ss199339651 Jul 04, 2010 (132)
36 BCM-HGSC-SUB ss208491175 Jul 04, 2010 (132)
37 1000GENOMES ss223783982 Jul 14, 2010 (132)
38 1000GENOMES ss234492316 Jul 15, 2010 (132)
39 1000GENOMES ss241337312 Jul 15, 2010 (132)
40 GMI ss279867288 May 04, 2012 (137)
41 GMI ss285867703 Apr 25, 2013 (138)
42 PJP ss294107745 May 09, 2011 (134)
43 ILLUMINA ss481426840 May 04, 2012 (137)
44 ILLUMINA ss481454144 May 04, 2012 (137)
45 ILLUMINA ss482434566 Sep 08, 2015 (146)
46 ILLUMINA ss485508433 May 04, 2012 (137)
47 ILLUMINA ss537420410 Sep 08, 2015 (146)
48 TISHKOFF ss560840915 Apr 25, 2013 (138)
49 SSMP ss655277410 Apr 25, 2013 (138)
50 ILLUMINA ss778959634 Sep 08, 2015 (146)
51 ILLUMINA ss783199764 Sep 08, 2015 (146)
52 ILLUMINA ss784154737 Sep 08, 2015 (146)
53 ILLUMINA ss825572234 Apr 01, 2015 (144)
54 ILLUMINA ss832459720 Sep 08, 2015 (146)
55 ILLUMINA ss834421559 Sep 08, 2015 (146)
56 EVA-GONL ss985672146 Aug 21, 2014 (142)
57 JMKIDD_LAB ss1075635674 Aug 21, 2014 (142)
58 1000GENOMES ss1330457105 Aug 21, 2014 (142)
59 HAMMER_LAB ss1397529717 Sep 08, 2015 (146)
60 DDI ss1431559443 Apr 01, 2015 (144)
61 EVA_GENOME_DK ss1582741887 Apr 01, 2015 (144)
62 EVA_DECODE ss1595272869 Apr 01, 2015 (144)
63 EVA_UK10K_ALSPAC ss1620956406 Apr 01, 2015 (144)
64 EVA_UK10K_TWINSUK ss1663950439 Apr 01, 2015 (144)
65 EVA_SVP ss1713046499 Apr 01, 2015 (144)
66 ILLUMINA ss1752741992 Sep 08, 2015 (146)
67 HAMMER_LAB ss1805600338 Sep 08, 2015 (146)
68 WEILL_CORNELL_DGM ss1928956979 Feb 12, 2016 (147)
69 ILLUMINA ss1946239605 Feb 12, 2016 (147)
70 ILLUMINA ss1959119755 Feb 12, 2016 (147)
71 GENOMED ss1971012329 Jul 19, 2016 (147)
72 JJLAB ss2025181365 Sep 14, 2016 (149)
73 USC_VALOUEV ss2153407008 Dec 20, 2016 (150)
74 HUMAN_LONGEVITY ss2304355048 Dec 20, 2016 (150)
75 TOPMED ss2474216565 Dec 20, 2016 (150)
76 SYSTEMSBIOZJU ss2627068744 Nov 08, 2017 (151)
77 ILLUMINA ss2634763464 Nov 08, 2017 (151)
78 GRF ss2709180632 Nov 08, 2017 (151)
79 ILLUMINA ss2711140599 Nov 08, 2017 (151)
80 GNOMAD ss2868495750 Nov 08, 2017 (151)
81 SWEGEN ss3003419259 Nov 08, 2017 (151)
82 ILLUMINA ss3022855609 Nov 08, 2017 (151)
83 BIOINF_KMB_FNS_UNIBA ss3026376614 Nov 08, 2017 (151)
84 CSHL ss3348247635 Nov 08, 2017 (151)
85 TOPMED ss3566128528 Nov 08, 2017 (151)
86 ILLUMINA ss3625954135 Oct 12, 2018 (152)
87 ILLUMINA ss3630088791 Oct 12, 2018 (152)
88 ILLUMINA ss3632661810 Oct 12, 2018 (152)
89 ILLUMINA ss3633505199 Oct 12, 2018 (152)
90 ILLUMINA ss3634232188 Oct 12, 2018 (152)
91 ILLUMINA ss3635177148 Oct 12, 2018 (152)
92 ILLUMINA ss3635910874 Oct 12, 2018 (152)
93 ILLUMINA ss3636915958 Oct 12, 2018 (152)
94 ILLUMINA ss3637664068 Oct 12, 2018 (152)
95 ILLUMINA ss3638767827 Oct 12, 2018 (152)
96 ILLUMINA ss3639386356 Oct 12, 2018 (152)
97 ILLUMINA ss3639722831 Oct 12, 2018 (152)
98 ILLUMINA ss3640884439 Oct 12, 2018 (152)
99 ILLUMINA ss3643698188 Oct 12, 2018 (152)
100 ILLUMINA ss3644972836 Oct 12, 2018 (152)
101 URBANLAB ss3648944151 Oct 12, 2018 (152)
102 ILLUMINA ss3653399006 Oct 12, 2018 (152)
103 1000Genomes NC_000008.10 - 75292492 Oct 12, 2018 (152)
104 The Avon Longitudinal Study of Parents and Children NC_000008.10 - 75292492 Oct 12, 2018 (152)
105 Genetic variation in the Estonian population NC_000008.10 - 75292492 Oct 12, 2018 (152)
106 gnomAD - Genomes NC_000008.10 - 75292492 Oct 12, 2018 (152)
107 TopMed NC_000008.11 - 74380257 Oct 12, 2018 (152)
108 UK 10K study - Twins NC_000008.10 - 75292492 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)
rs17257763 Oct 08, 2004 (123)
rs59969260 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss76420479, ss77150209, ss93911054, ss108132447, ss113231370, ss116016311, ss165011590, ss166775432, ss199339651, ss208491175, ss279867288, ss285867703, ss294107745, ss481426840, ss825572234, ss1397529717, ss1595272869, ss1713046499, ss3639386356, ss3639722831, ss3643698188 NC_000008.9:75455046:C:T NC_000008.11:74380256:C:T (self)
42602246, 23694905, 16848367, 209123504, 23694905, ss223783982, ss234492316, ss241337312, ss481454144, ss482434566, ss485508433, ss537420410, ss560840915, ss655277410, ss778959634, ss783199764, ss784154737, ss832459720, ss834421559, ss985672146, ss1075635674, ss1330457105, ss1431559443, ss1582741887, ss1620956406, ss1663950439, ss1752741992, ss1805600338, ss1928956979, ss1946239605, ss1959119755, ss1971012329, ss2025181365, ss2153407008, ss2474216565, ss2627068744, ss2634763464, ss2709180632, ss2711140599, ss2868495750, ss3003419259, ss3022855609, ss3348247635, ss3625954135, ss3630088791, ss3632661810, ss3633505199, ss3634232188, ss3635177148, ss3635910874, ss3636915958, ss3637664068, ss3638767827, ss3640884439, ss3644972836, ss3653399006 NC_000008.10:75292491:C:T NC_000008.11:74380256:C:T (self)
392876507, ss2304355048, ss3026376614, ss3566128528, ss3648944151 NC_000008.11:74380256:C:T NC_000008.11:74380256:C:T (self)
ss10450739 NT_008183.16:27135041:C:T NC_000008.11:74380256:C:T (self)
ss15690774, ss20340668, ss22743694 NT_008183.17:27135041:C:T NC_000008.11:74380256:C:T (self)
ss14898793, ss24528756, ss44923642, ss65973560, ss66848859, ss67527137, ss67895323, ss70901163, ss71496519, ss75873418, ss79241716, ss84593456, ss97881833, ss122665393, ss134335562, ss143566785, ss154397353, ss156521187, ss159572767, ss160835003, ss172230102, ss174198601 NT_008183.19:27156892:C:T NC_000008.11:74380256:C:T (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 rs6996971
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