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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.

rs72793807

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr16:28640411 (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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.230103 (60906/264690, TOPMED)
T=0.241238 (33769/139982, GnomAD)
T=0.28025 (7040/25120, ALFA) (+ 12 more)
T=0.17607 (2951/16760, 8.3KJPN)
T=0.1819 (911/5008, 1000G)
T=0.2774 (1069/3854, ALSPAC)
T=0.2891 (1072/3708, TWINSUK)
T=0.1676 (491/2930, KOREAN)
T=0.1698 (311/1832, Korea1K)
T=0.267 (266/998, GoNL)
T=0.283 (170/600, NorthernSweden)
C=0.428 (95/222, SGDP_PRJ)
T=0.102 (22/216, Qatari)
T=0.38 (15/40, GENOME_DK)
C=0.40 (8/20, Siberian)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
NPIPB8 : 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 16 NC_000016.10:g.28640411C>T
GRCh37.p13 chr 16 NC_000016.9:g.28651732C>T
Gene: NPIPB8, nuclear pore complex interacting protein family member B8 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
NPIPB8 transcript variant 1 NM_001310136.2:c.120+1931…

NM_001310136.2:c.120+1931C>T

N/A Intron Variant
NPIPB8 transcript variant 2 NM_001385922.1:c.120+1931…

NM_001385922.1:c.120+1931C>T

N/A Intron Variant
NPIPB8 transcript variant X1 XM_017023622.1:c.120+1931…

XM_017023622.1:c.120+1931C>T

N/A Intron Variant
NPIPB8 transcript variant X2 XM_017023623.1:c.120+1931…

XM_017023623.1:c.120+1931C>T

N/A Intron Variant
NPIPB8 transcript variant X5 XM_017023625.1:c.25+1931C…

XM_017023625.1:c.25+1931C>T

N/A Intron Variant
NPIPB8 transcript variant X6 XM_017023626.1:c.-693+193…

XM_017023626.1:c.-693+1931C>T

N/A Intron Variant
NPIPB8 transcript variant X7 XM_024450416.1:c.-300+193…

XM_024450416.1:c.-300+1931C>T

N/A Intron Variant
NPIPB8 transcript variant X8 XM_024450417.1:c.-312-929…

XM_024450417.1:c.-312-929C>T

N/A Intron Variant
NPIPB8 transcript variant X9 XM_024450418.1:c.-693+193…

XM_024450418.1:c.-693+1931C>T

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
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 25120 C=0.71975 T=0.28025
European Sub 20266 C=0.70004 T=0.29996
African Sub 2946 C=0.8198 T=0.1802
African Others Sub 114 C=0.833 T=0.167
African American Sub 2832 C=0.8192 T=0.1808
Asian Sub 112 C=0.884 T=0.116
East Asian Sub 86 C=0.90 T=0.10
Other Asian Sub 26 C=0.85 T=0.15
Latin American 1 Sub 146 C=0.822 T=0.178
Latin American 2 Sub 610 C=0.733 T=0.267
South Asian Sub 98 C=0.92 T=0.08
Other Sub 942 C=0.766 T=0.234


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 C=0.769897 T=0.230103
gnomAD - Genomes Global Study-wide 139982 C=0.758762 T=0.241238
gnomAD - Genomes European Sub 75836 C=0.71157 T=0.28843
gnomAD - Genomes African Sub 41922 C=0.82832 T=0.17168
gnomAD - Genomes American Sub 13632 C=0.78338 T=0.21662
gnomAD - Genomes Ashkenazi Jewish Sub 3322 C=0.7258 T=0.2742
gnomAD - Genomes East Asian Sub 3124 C=0.8816 T=0.1184
gnomAD - Genomes Other Sub 2146 C=0.7833 T=0.2167
8.3KJPN JAPANESE Study-wide 16760 C=0.82393 T=0.17607
1000Genomes Global Study-wide 5008 C=0.8181 T=0.1819
1000Genomes African Sub 1322 C=0.8374 T=0.1626
1000Genomes East Asian Sub 1008 C=0.8631 T=0.1369
1000Genomes Europe Sub 1006 C=0.7614 T=0.2386
1000Genomes South Asian Sub 978 C=0.856 T=0.144
1000Genomes American Sub 694 C=0.745 T=0.255
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.7226 T=0.2774
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.7109 T=0.2891
KOREAN population from KRGDB KOREAN Study-wide 2930 C=0.8324 T=0.1676
Korean Genome Project KOREAN Study-wide 1832 C=0.8302 T=0.1698
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.733 T=0.267
Northern Sweden ACPOP Study-wide 600 C=0.717 T=0.283
SGDP_PRJ Global Study-wide 222 C=0.428 T=0.572
Qatari Global Study-wide 216 C=0.898 T=0.102
The Danish reference pan genome Danish Study-wide 40 C=0.62 T=0.38
Siberian Global Study-wide 20 C=0.40 T=0.60
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
GRCh38.p13 chr 16 NC_000016.10:g.28640411= NC_000016.10:g.28640411C>T
GRCh37.p13 chr 16 NC_000016.9:g.28651732= NC_000016.9:g.28651732C>T
NPIPB8 transcript variant 1 NM_001310136.2:c.120+1931= NM_001310136.2:c.120+1931C>T
NPIPB8 transcript variant 2 NM_001385922.1:c.120+1931= NM_001385922.1:c.120+1931C>T
NPIPB8 transcript variant X1 XM_017023622.1:c.120+1931= XM_017023622.1:c.120+1931C>T
NPIPB8 transcript variant X2 XM_017023623.1:c.120+1931= XM_017023623.1:c.120+1931C>T
NPIPB8 transcript variant X5 XM_017023625.1:c.25+1931= XM_017023625.1:c.25+1931C>T
NPIPB8 transcript variant X6 XM_017023626.1:c.-693+1931= XM_017023626.1:c.-693+1931C>T
NPIPB8 transcript variant X7 XM_024450416.1:c.-300+1931= XM_024450416.1:c.-300+1931C>T
NPIPB8 transcript variant X8 XM_024450417.1:c.-312-929= XM_024450417.1:c.-312-929C>T
NPIPB8 transcript variant X9 XM_024450418.1:c.-693+1931= XM_024450418.1:c.-693+1931C>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#.

48 SubSNP, 15 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss109294020 Feb 13, 2009 (130)
2 COMPLETE_GENOMICS ss168101583 Jul 04, 2010 (132)
3 BUSHMAN ss201601331 Jul 04, 2010 (132)
4 1000GENOMES ss227211551 Jul 14, 2010 (132)
5 1000GENOMES ss237002539 Jul 15, 2010 (132)
6 1000GENOMES ss243346969 Jul 15, 2010 (132)
7 BL ss255613871 May 09, 2011 (134)
8 GMI ss282489876 May 04, 2012 (137)
9 GMI ss287057519 Apr 25, 2013 (138)
10 ILLUMINA ss533235154 Sep 08, 2015 (146)
11 TISHKOFF ss564864859 Apr 25, 2013 (138)
12 SSMP ss660617126 Apr 25, 2013 (138)
13 EVA-GONL ss992420928 Aug 21, 2014 (142)
14 1000GENOMES ss1355923578 Aug 21, 2014 (142)
15 DDI ss1427820661 Apr 01, 2015 (144)
16 EVA_GENOME_DK ss1577891457 Apr 01, 2015 (144)
17 EVA_UK10K_ALSPAC ss1634284320 Apr 01, 2015 (144)
18 EVA_UK10K_TWINSUK ss1677278353 Apr 01, 2015 (144)
19 HAMMER_LAB ss1808484499 Sep 08, 2015 (146)
20 WEILL_CORNELL_DGM ss1935844809 Feb 12, 2016 (147)
21 GENOMED ss1968249540 Jul 19, 2016 (147)
22 JJLAB ss2028710659 Sep 14, 2016 (149)
23 ILLUMINA ss2094889200 Dec 20, 2016 (150)
24 ILLUMINA ss2095065344 Dec 20, 2016 (150)
25 USC_VALOUEV ss2157123409 Dec 20, 2016 (150)
26 TOPMED ss2376409784 Dec 20, 2016 (150)
27 SYSTEMSBIOZJU ss2628848074 Nov 08, 2017 (151)
28 GRF ss2701629581 Nov 08, 2017 (151)
29 GNOMAD ss2941924120 Nov 08, 2017 (151)
30 AFFY ss2985065122 Nov 08, 2017 (151)
31 AFFY ss2985702855 Nov 08, 2017 (151)
32 SWEGEN ss3014307741 Nov 08, 2017 (151)
33 BIOINF_KMB_FNS_UNIBA ss3028179022 Nov 08, 2017 (151)
34 TOPMED ss3243775895 Nov 08, 2017 (151)
35 CSHL ss3351403178 Nov 08, 2017 (151)
36 ILLUMINA ss3627508436 Oct 12, 2018 (152)
37 ILLUMINA ss3652104964 Oct 12, 2018 (152)
38 ILLUMINA ss3653837693 Oct 12, 2018 (152)
39 EVA_DECODE ss3699111504 Jul 13, 2019 (153)
40 ACPOP ss3741455542 Jul 13, 2019 (153)
41 EVA ss3753849135 Jul 13, 2019 (153)
42 KHV_HUMAN_GENOMES ss3819143095 Jul 13, 2019 (153)
43 EVA ss3834542099 Apr 27, 2020 (154)
44 SGDP_PRJ ss3884253920 Apr 27, 2020 (154)
45 KRGDB ss3933596139 Apr 27, 2020 (154)
46 KOGIC ss3977372201 Apr 27, 2020 (154)
47 TOPMED ss5012339901 Apr 27, 2021 (155)
48 TOMMO_GENOMICS ss5219106217 Apr 27, 2021 (155)
49 1000Genomes NC_000016.9 - 28651732 Oct 12, 2018 (152)
50 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 28651732 Oct 12, 2018 (152)
51 The Danish reference pan genome NC_000016.9 - 28651732 Apr 27, 2020 (154)
52 gnomAD - Genomes NC_000016.10 - 28640411 Apr 27, 2021 (155)
53 Genome of the Netherlands Release 5 NC_000016.9 - 28651732 Apr 27, 2020 (154)
54 KOREAN population from KRGDB NC_000016.9 - 28651732 Apr 27, 2020 (154)
55 Korean Genome Project NC_000016.10 - 28640411 Apr 27, 2020 (154)
56 Northern Sweden NC_000016.9 - 28651732 Jul 13, 2019 (153)
57 Qatari NC_000016.9 - 28651732 Apr 27, 2020 (154)
58 SGDP_PRJ NC_000016.9 - 28651732 Apr 27, 2020 (154)
59 Siberian NC_000016.9 - 28651732 Apr 27, 2020 (154)
60 8.3KJPN NC_000016.9 - 28651732 Apr 27, 2021 (155)
61 TopMed NC_000016.10 - 28640411 Apr 27, 2021 (155)
62 UK 10K study - Twins NC_000016.9 - 28651732 Oct 12, 2018 (152)
63 ALFA NC_000016.10 - 28640411 Apr 27, 2021 (155)
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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss109294020, ss168101583, ss201601331, ss255613871, ss282489876, ss287057519, ss2094889200 NC_000016.8:28559232:C:T NC_000016.10:28640410:C:T (self)
69076647, 38347056, 4104825, 17104586, 40773533, 14740407, 17886731, 36270900, 9639763, 77075524, 38347056, ss227211551, ss237002539, ss243346969, ss533235154, ss564864859, ss660617126, ss992420928, ss1355923578, ss1427820661, ss1577891457, ss1634284320, ss1677278353, ss1808484499, ss1935844809, ss1968249540, ss2028710659, ss2095065344, ss2157123409, ss2376409784, ss2628848074, ss2701629581, ss2941924120, ss2985065122, ss2985702855, ss3014307741, ss3351403178, ss3627508436, ss3652104964, ss3653837693, ss3741455542, ss3753849135, ss3834542099, ss3884253920, ss3933596139, ss5219106217 NC_000016.9:28651731:C:T NC_000016.10:28640410:C:T (self)
486848094, 33750202, 142376842, 227885562, 13977110214, ss3028179022, ss3243775895, ss3699111504, ss3819143095, ss3977372201, ss5012339901 NC_000016.10:28640410:C:T NC_000016.10:28640410: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.

No publications for rs72793807

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