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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.

rs10764638

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr10:26742285 (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
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.385508 (102040/264690, TOPMED)
A=0.399642 (56009/140148, GnomAD)
A=0.47421 (12170/25664, ALFA) (+ 15 more)
A=0.42906 (7191/16760, 8.3KJPN)
A=0.3231 (1618/5008, 1000G)
G=0.4444 (1991/4480, Estonian)
G=0.4328 (1668/3854, ALSPAC)
G=0.4393 (1629/3708, TWINSUK)
A=0.3754 (1100/2930, KOREAN)
A=0.3216 (568/1766, HapMap)
G=0.451 (450/998, GoNL)
A=0.500 (300/600, NorthernSweden)
G=0.500 (300/600, NorthernSweden)
A=0.250 (117/468, SGDP_PRJ)
A=0.301 (65/216, Qatari)
A=0.352 (76/216, Vietnamese)
A=0.27 (13/48, Siberian)
A=0.45 (18/40, GENOME_DK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PDSS1 : 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.p13 chr 10 NC_000010.11:g.26742285A>G
GRCh37.p13 chr 10 NC_000010.10:g.27031214A>G
PDSS1 RefSeqGene NG_008972.2:g.49620A>G
Gene: PDSS1, decaprenyl diphosphate synthase subunit 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
PDSS1 transcript variant 2 NM_001321978.2:c.836-212A…

NM_001321978.2:c.836-212A>G

N/A Intron Variant
PDSS1 transcript variant 3 NM_001321979.2:c.517-212A…

NM_001321979.2:c.517-212A>G

N/A Intron Variant
PDSS1 transcript variant 1 NM_014317.5:c.1027-212A>G N/A Intron Variant
PDSS1 transcript variant X3 XM_011519437.3:c.658-212A…

XM_011519437.3:c.658-212A>G

N/A Intron Variant
PDSS1 transcript variant X2 XM_017016011.2:c.706-212A…

XM_017016011.2:c.706-212A>G

N/A Intron Variant
PDSS1 transcript variant X5 XM_024447923.1:c.517-212A…

XM_024447923.1:c.517-212A>G

N/A Intron Variant
PDSS1 transcript variant X1 XM_024447922.1:c. N/A Genic Downstream Transcript Variant
PDSS1 transcript variant X4 XR_428636.4: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.

Allele: G (allele ID: 665099 )
ClinVar Accession Disease Names Clinical Significance
RCV000843613.1 not provided Benign

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 25664 A=0.47421 G=0.52579
European Sub 17398 A=0.55662 G=0.44338
African Sub 3622 A=0.1115 G=0.8885
African Others Sub 126 A=0.040 G=0.960
African American Sub 3496 A=0.1141 G=0.8859
Asian Sub 160 A=0.350 G=0.650
East Asian Sub 102 A=0.363 G=0.637
Other Asian Sub 58 A=0.33 G=0.67
Latin American 1 Sub 290 A=0.403 G=0.597
Latin American 2 Sub 2740 A=0.4719 G=0.5281
South Asian Sub 110 A=0.364 G=0.636
Other Sub 1344 A=0.4286 G=0.5714


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 A=0.385508 G=0.614492
gnomAD - Genomes Global Study-wide 140148 A=0.399642 G=0.600358
gnomAD - Genomes European Sub 75852 A=0.55172 G=0.44828
gnomAD - Genomes African Sub 42038 A=0.11273 G=0.88727
gnomAD - Genomes American Sub 13652 A=0.44038 G=0.55962
gnomAD - Genomes Ashkenazi Jewish Sub 3324 A=0.4504 G=0.5496
gnomAD - Genomes East Asian Sub 3130 A=0.3288 G=0.6712
gnomAD - Genomes Other Sub 2152 A=0.4103 G=0.5897
8.3KJPN JAPANESE Study-wide 16760 A=0.42906 G=0.57094
1000Genomes Global Study-wide 5008 A=0.3231 G=0.6769
1000Genomes African Sub 1322 A=0.0401 G=0.9599
1000Genomes East Asian Sub 1008 A=0.3720 G=0.6280
1000Genomes Europe Sub 1006 A=0.5030 G=0.4970
1000Genomes South Asian Sub 978 A=0.392 G=0.608
1000Genomes American Sub 694 A=0.434 G=0.566
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.5556 G=0.4444
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.5672 G=0.4328
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.5607 G=0.4393
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.3754 G=0.6246
HapMap Global Study-wide 1766 A=0.3216 G=0.6784
HapMap American Sub 766 A=0.428 G=0.572
HapMap African Sub 570 A=0.091 G=0.909
HapMap Asian Sub 254 A=0.406 G=0.594
HapMap Europe Sub 176 A=0.483 G=0.517
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.549 G=0.451
Northern Sweden ACPOP Study-wide 600 A=0.500 G=0.500
SGDP_PRJ Global Study-wide 468 A=0.250 G=0.750
Qatari Global Study-wide 216 A=0.301 G=0.699
A Vietnamese Genetic Variation Database Global Study-wide 216 A=0.352 G=0.648
Siberian Global Study-wide 48 A=0.27 G=0.73
The Danish reference pan genome Danish Study-wide 40 A=0.45 G=0.55
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
GRCh38.p13 chr 10 NC_000010.11:g.26742285= NC_000010.11:g.26742285A>G
GRCh37.p13 chr 10 NC_000010.10:g.27031214= NC_000010.10:g.27031214A>G
PDSS1 RefSeqGene NG_008972.2:g.49620= NG_008972.2:g.49620A>G
PDSS1 transcript variant 2 NM_001321978.2:c.836-212= NM_001321978.2:c.836-212A>G
PDSS1 transcript variant 3 NM_001321979.2:c.517-212= NM_001321979.2:c.517-212A>G
PDSS1 transcript NM_014317.3:c.1027-212= NM_014317.3:c.1027-212A>G
PDSS1 transcript variant 1 NM_014317.5:c.1027-212= NM_014317.5:c.1027-212A>G
PDSS1 transcript variant X1 XM_005252438.1:c.836-212= XM_005252438.1:c.836-212A>G
PDSS1 transcript variant X2 XM_005252439.1:c.517-212= XM_005252439.1:c.517-212A>G
PDSS1 transcript variant X3 XM_011519437.3:c.658-212= XM_011519437.3:c.658-212A>G
PDSS1 transcript variant X2 XM_017016011.2:c.706-212= XM_017016011.2:c.706-212A>G
PDSS1 transcript variant X5 XM_024447923.1:c.517-212= XM_024447923.1:c.517-212A>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#.

70 SubSNP, 17 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss15874092 Feb 27, 2004 (120)
2 CSHL-HAPMAP ss17378623 Feb 27, 2004 (120)
3 SC_SNP ss18406845 Feb 27, 2004 (120)
4 SC_SNP ss18860248 Feb 27, 2004 (120)
5 ABI ss38572955 Mar 14, 2006 (126)
6 AFFY ss66204380 Nov 29, 2006 (127)
7 AFFY ss76295574 Dec 07, 2007 (129)
8 HGSV ss82335849 Dec 15, 2007 (130)
9 KRIBB_YJKIM ss82758467 Dec 14, 2007 (130)
10 HUMANGENOME_JCVI ss97632210 Feb 05, 2009 (130)
11 BGI ss106664436 Feb 05, 2009 (130)
12 1000GENOMES ss109323026 Jan 23, 2009 (130)
13 1000GENOMES ss115450981 Jan 25, 2009 (130)
14 ILLUMINA-UK ss119097022 Feb 15, 2009 (130)
15 ENSEMBL ss138719996 Dec 01, 2009 (131)
16 GMI ss154740444 Dec 01, 2009 (131)
17 COMPLETE_GENOMICS ss169465633 Jul 04, 2010 (132)
18 AFFY ss173162272 Jul 04, 2010 (132)
19 BUSHMAN ss201304829 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss207290727 Jul 04, 2010 (132)
21 1000GENOMES ss224637416 Jul 14, 2010 (132)
22 1000GENOMES ss235107379 Jul 15, 2010 (132)
23 1000GENOMES ss241828394 Jul 15, 2010 (132)
24 GMI ss280530077 May 04, 2012 (137)
25 GMI ss286151648 Apr 25, 2013 (138)
26 PJP ss291000379 May 09, 2011 (134)
27 TISHKOFF ss561854334 Apr 25, 2013 (138)
28 SSMP ss656456331 Apr 25, 2013 (138)
29 EVA-GONL ss987322479 Aug 21, 2014 (142)
30 JMKIDD_LAB ss1076861907 Aug 21, 2014 (142)
31 1000GENOMES ss1336771805 Aug 21, 2014 (142)
32 DDI ss1426261481 Apr 01, 2015 (144)
33 EVA_GENOME_DK ss1575001447 Apr 01, 2015 (144)
34 EVA_DECODE ss1596983316 Apr 01, 2015 (144)
35 EVA_UK10K_ALSPAC ss1624248473 Apr 01, 2015 (144)
36 EVA_UK10K_TWINSUK ss1667242506 Apr 01, 2015 (144)
37 EVA_SVP ss1713167842 Apr 01, 2015 (144)
38 HAMMER_LAB ss1806316192 Sep 08, 2015 (146)
39 WEILL_CORNELL_DGM ss1930654391 Feb 12, 2016 (147)
40 GENOMED ss1967088838 Jul 19, 2016 (147)
41 JJLAB ss2026055663 Sep 14, 2016 (149)
42 USC_VALOUEV ss2154300665 Dec 20, 2016 (150)
43 HUMAN_LONGEVITY ss2173658009 Dec 20, 2016 (150)
44 TOPMED ss2336400640 Dec 20, 2016 (150)
45 SYSTEMSBIOZJU ss2627497292 Nov 08, 2017 (151)
46 GRF ss2698532715 Nov 08, 2017 (151)
47 GNOMAD ss2886891049 Nov 08, 2017 (151)
48 SWEGEN ss3006143424 Nov 08, 2017 (151)
49 BIOINF_KMB_FNS_UNIBA ss3026814233 Nov 08, 2017 (151)
50 TOPMED ss3114748703 Nov 08, 2017 (151)
51 CSHL ss3349023490 Nov 08, 2017 (151)
52 URBANLAB ss3649320012 Oct 12, 2018 (152)
53 EGCUT_WGS ss3673667986 Jul 13, 2019 (153)
54 EVA_DECODE ss3689531656 Jul 13, 2019 (153)
55 ACPOP ss3737172271 Jul 13, 2019 (153)
56 EVA ss3747901118 Jul 13, 2019 (153)
57 PACBIO ss3786618895 Jul 13, 2019 (153)
58 PACBIO ss3791806504 Jul 13, 2019 (153)
59 PACBIO ss3796688463 Jul 13, 2019 (153)
60 KHV_HUMAN_GENOMES ss3813265126 Jul 13, 2019 (153)
61 EVA ss3832034942 Apr 26, 2020 (154)
62 EVA ss3839549667 Apr 26, 2020 (154)
63 EVA ss3845016916 Apr 26, 2020 (154)
64 SGDP_PRJ ss3873804967 Apr 26, 2020 (154)
65 KRGDB ss3921771832 Apr 26, 2020 (154)
66 FSA-LAB ss3983974923 Apr 26, 2021 (155)
67 EVA ss3986479509 Apr 26, 2021 (155)
68 TOPMED ss4846604284 Apr 26, 2021 (155)
69 TOMMO_GENOMICS ss5196823635 Apr 26, 2021 (155)
70 EVA ss5237208135 Apr 26, 2021 (155)
71 1000Genomes NC_000010.10 - 27031214 Oct 12, 2018 (152)
72 The Avon Longitudinal Study of Parents and Children NC_000010.10 - 27031214 Oct 12, 2018 (152)
73 Genetic variation in the Estonian population NC_000010.10 - 27031214 Oct 12, 2018 (152)
74 The Danish reference pan genome NC_000010.10 - 27031214 Apr 26, 2020 (154)
75 gnomAD - Genomes NC_000010.11 - 26742285 Apr 26, 2021 (155)
76 Genome of the Netherlands Release 5 NC_000010.10 - 27031214 Apr 26, 2020 (154)
77 HapMap NC_000010.11 - 26742285 Apr 26, 2020 (154)
78 KOREAN population from KRGDB NC_000010.10 - 27031214 Apr 26, 2020 (154)
79 Northern Sweden NC_000010.10 - 27031214 Jul 13, 2019 (153)
80 Qatari NC_000010.10 - 27031214 Apr 26, 2020 (154)
81 SGDP_PRJ NC_000010.10 - 27031214 Apr 26, 2020 (154)
82 Siberian NC_000010.10 - 27031214 Apr 26, 2020 (154)
83 8.3KJPN NC_000010.10 - 27031214 Apr 26, 2021 (155)
84 TopMed NC_000010.11 - 26742285 Apr 26, 2021 (155)
85 UK 10K study - Twins NC_000010.10 - 27031214 Oct 12, 2018 (152)
86 A Vietnamese Genetic Variation Database NC_000010.10 - 27031214 Jul 13, 2019 (153)
87 ALFA NC_000010.11 - 26742285 Apr 26, 2021 (155)
88 ClinVar RCV000843613.1 Apr 26, 2020 (154)
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)
rs56800250 Feb 27, 2009 (130)
rs59789997 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss82335849 NC_000010.8:27071219:A:G NC_000010.11:26742284:A:G (self)
ss109323026, ss115450981, ss119097022, ss169465633, ss201304829, ss207290727, ss280530077, ss286151648, ss291000379, ss1596983316, ss1713167842 NC_000010.9:27071219:A:G NC_000010.11:26742284:A:G (self)
49135871, 27301871, 19406234, 2084928, 12172730, 28949226, 10457136, 12696321, 25821947, 6817019, 54792942, 27301871, 6062203, ss224637416, ss235107379, ss241828394, ss561854334, ss656456331, ss987322479, ss1076861907, ss1336771805, ss1426261481, ss1575001447, ss1624248473, ss1667242506, ss1806316192, ss1930654391, ss1967088838, ss2026055663, ss2154300665, ss2336400640, ss2627497292, ss2698532715, ss2886891049, ss3006143424, ss3349023490, ss3673667986, ss3737172271, ss3747901118, ss3786618895, ss3791806504, ss3796688463, ss3832034942, ss3839549667, ss3873804967, ss3921771832, ss3983974923, ss3986479509, ss5196823635 NC_000010.10:27031213:A:G NC_000010.11:26742284:A:G (self)
RCV000843613.1, 346963787, 367068, 39067621, 62149939, 6212071685, ss2173658009, ss3026814233, ss3114748703, ss3649320012, ss3689531656, ss3813265126, ss3845016916, ss4846604284, ss5237208135 NC_000010.11:26742284:A:G NC_000010.11:26742284:A:G (self)
ss15874092, ss17378623, ss18406845, ss18860248 NT_008705.15:9006538:A:G NC_000010.11:26742284:A:G (self)
ss38572955, ss66204380, ss76295574, ss82758467, ss97632210, ss106664436, ss138719996, ss154740444, ss173162272 NT_008705.16:26971213:A:G NC_000010.11:26742284: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.

No publications for rs10764638

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