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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.

rs4468641

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr16:31085555 (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>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.45677 (57356/125568, TOPMED)
C=0.4592 (14364/31282, GnomAD)
C=0.498 (2493/5008, 1000G) (+ 5 more)
C=0.422 (1890/4480, Estonian)
C=0.382 (1474/3854, ALSPAC)
C=0.388 (1438/3708, TWINSUK)
C=0.43 (260/600, NorthernSweden)
C=0.14 (31/214, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
PRSS53 : 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 16 NC_000016.10:g.31085555A>C
GRCh37.p13 chr 16 NC_000016.9:g.31096876A>C
Gene: PRSS53, serine protease 53 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PRSS53 transcript NM_001039503.2:c. N/A Intron Variant
PRSS53 transcript variant X1 XM_011545816.2:c. N/A Intron Variant
PRSS53 transcript variant X2 XM_011545817.2:c. N/A Intron Variant
PRSS53 transcript variant X3 XM_011545818.3:c. N/A Intron Variant
PRSS53 transcript variant X4 XM_011545819.2:c. N/A Intron Variant
PRSS53 transcript variant X5 XM_011545820.2: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").

Download
Study Population Group Sample Size Ref Allele Alt Allele
TopMed Global Study-wide 125568 A=0.54323 C=0.45677
gnomAD - Genomes Global Study-wide 31282 A=0.5408 C=0.4592
gnomAD - Genomes European Sub 18846 A=0.6051 C=0.3949
gnomAD - Genomes African Sub 8658 A=0.324 C=0.676
gnomAD - Genomes East Asian Sub 1556 A=0.900 C=0.100
gnomAD - Genomes Other Sub 1086 A=0.574 C=0.426
gnomAD - Genomes American Sub 846 A=0.59 C=0.41
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=0.67 C=0.33
1000Genomes Global Study-wide 5008 A=0.502 C=0.498
1000Genomes African Sub 1322 A=0.279 C=0.721
1000Genomes East Asian Sub 1008 A=0.888 C=0.112
1000Genomes Europe Sub 1006 A=0.623 C=0.377
1000Genomes South Asian Sub 978 A=0.24 C=0.76
1000Genomes American Sub 694 A=0.56 C=0.44
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.578 C=0.422
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.618 C=0.382
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.612 C=0.388
Northern Sweden ACPOP Study-wide 600 A=0.57 C=0.43
A Vietnamese Genetic Variation Database Global Study-wide 214 A=0.86 C=0.14
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= C Note
GRCh38.p12 chr 16 NC_000016.10:g.31085555= NC_000016.10:g.31085555A>C
GRCh37.p13 chr 16 NC_000016.9:g.31096876= NC_000016.9:g.31096876A>C
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#.

85 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_JCM ss6003349 Feb 20, 2003 (111)
2 CSHL-HAPMAP ss17564152 Feb 27, 2004 (120)
3 CSHL-HAPMAP ss19344962 Feb 27, 2004 (120)
4 ABI ss43969109 Mar 13, 2006 (126)
5 ILLUMINA ss74963683 Dec 06, 2007 (129)
6 HGSV ss77131322 Dec 06, 2007 (129)
7 HGSV ss84200086 Dec 15, 2007 (130)
8 BGI ss103290718 Dec 01, 2009 (131)
9 1000GENOMES ss109298601 Jan 23, 2009 (130)
10 1000GENOMES ss115026844 Jan 25, 2009 (130)
11 ILLUMINA-UK ss118236112 Feb 14, 2009 (130)
12 KRIBB_YJKIM ss119477699 Dec 01, 2009 (131)
13 ILLUMINA ss160681541 Dec 01, 2009 (131)
14 ENSEMBL ss161771435 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss168117777 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss169573610 Jul 04, 2010 (132)
17 COMPLETE_GENOMICS ss171172263 Jul 04, 2010 (132)
18 ILLUMINA ss173738367 Jul 04, 2010 (132)
19 BUSHMAN ss201611258 Jul 04, 2010 (132)
20 BCM-HGSC-SUB ss207622104 Jul 04, 2010 (132)
21 1000GENOMES ss227214741 Jul 14, 2010 (132)
22 1000GENOMES ss237004889 Jul 15, 2010 (132)
23 1000GENOMES ss243348934 Jul 15, 2010 (132)
24 BL ss255620513 May 09, 2011 (134)
25 PJP ss291944762 May 09, 2011 (134)
26 ILLUMINA ss480952377 May 04, 2012 (137)
27 ILLUMINA ss480972148 May 04, 2012 (137)
28 ILLUMINA ss481940478 Sep 08, 2015 (146)
29 ILLUMINA ss485271116 May 04, 2012 (137)
30 ILLUMINA ss537238627 Sep 08, 2015 (146)
31 TISHKOFF ss564870493 Apr 25, 2013 (138)
32 SSMP ss660625280 Apr 25, 2013 (138)
33 ILLUMINA ss778908986 Sep 08, 2015 (146)
34 ILLUMINA ss783081486 Sep 08, 2015 (146)
35 ILLUMINA ss784039100 Sep 08, 2015 (146)
36 ILLUMINA ss832339824 Sep 08, 2015 (146)
37 ILLUMINA ss834370319 Sep 08, 2015 (146)
38 EVA-GONL ss992432542 Aug 21, 2014 (142)
39 JMKIDD_LAB ss1080589001 Aug 21, 2014 (142)
40 1000GENOMES ss1355977116 Aug 21, 2014 (142)
41 DDI ss1427823799 Apr 01, 2015 (144)
42 EVA_GENOME_DK ss1577894818 Apr 01, 2015 (144)
43 EVA_UK10K_ALSPAC ss1634304693 Apr 01, 2015 (144)
44 EVA_UK10K_TWINSUK ss1677298726 Apr 01, 2015 (144)
45 EVA_DECODE ss1696466949 Apr 01, 2015 (144)
46 EVA_SVP ss1713536018 Apr 01, 2015 (144)
47 ILLUMINA ss1752190345 Sep 08, 2015 (146)
48 HAMMER_LAB ss1808488882 Sep 08, 2015 (146)
49 WEILL_CORNELL_DGM ss1935857447 Feb 12, 2016 (147)
50 GENOMED ss1968250975 Jul 19, 2016 (147)
51 JJLAB ss2028715702 Sep 14, 2016 (149)
52 ILLUMINA ss2094890056 Dec 20, 2016 (150)
53 ILLUMINA ss2095066077 Dec 20, 2016 (150)
54 USC_VALOUEV ss2157129948 Dec 20, 2016 (150)
55 HUMAN_LONGEVITY ss2211737687 Dec 20, 2016 (150)
56 TOPMED ss2376533899 Dec 20, 2016 (150)
57 ILLUMINA ss2633311800 Nov 08, 2017 (151)
58 GRF ss2701637526 Nov 08, 2017 (151)
59 GNOMAD ss2942118930 Nov 08, 2017 (151)
60 AFFY ss2985066748 Nov 08, 2017 (151)
61 SWEGEN ss3014335102 Nov 08, 2017 (151)
62 BIOINF_KMB_FNS_UNIBA ss3028180738 Nov 08, 2017 (151)
63 TOPMED ss3244230971 Nov 08, 2017 (151)
64 CSHL ss3351408481 Nov 08, 2017 (151)
65 ILLUMINA ss3627511056 Oct 12, 2018 (152)
66 ILLUMINA ss3631298611 Oct 12, 2018 (152)
67 ILLUMINA ss3633825125 Oct 12, 2018 (152)
68 ILLUMINA ss3634639898 Oct 12, 2018 (152)
69 ILLUMINA ss3635513469 Oct 12, 2018 (152)
70 ILLUMINA ss3636330221 Oct 12, 2018 (152)
71 ILLUMINA ss3637264895 Oct 12, 2018 (152)
72 ILLUMINA ss3638122201 Oct 12, 2018 (152)
73 ILLUMINA ss3640347217 Oct 12, 2018 (152)
74 ILLUMINA ss3641070960 Oct 12, 2018 (152)
75 ILLUMINA ss3641366445 Oct 12, 2018 (152)
76 ILLUMINA ss3643103526 Oct 12, 2018 (152)
77 ILLUMINA ss3652107619 Oct 12, 2018 (152)
78 EGCUT_WGS ss3681408824 Jul 13, 2019 (153)
79 EVA_DECODE ss3699138460 Jul 13, 2019 (153)
80 ACPOP ss3741465792 Jul 13, 2019 (153)
81 ILLUMINA ss3744431309 Jul 13, 2019 (153)
82 ILLUMINA ss3744940326 Jul 13, 2019 (153)
83 EVA ss3753863620 Jul 13, 2019 (153)
84 ILLUMINA ss3772438628 Jul 13, 2019 (153)
85 KHV_HUMAN_GENOMES ss3819156684 Jul 13, 2019 (153)
86 1000Genomes NC_000016.9 - 31096876 Oct 12, 2018 (152)
87 The Avon Longitudinal Study of Parents and Children NC_000016.9 - 31096876 Oct 12, 2018 (152)
88 Genetic variation in the Estonian population NC_000016.9 - 31096876 Oct 12, 2018 (152)
89 gnomAD - Genomes NC_000016.9 - 31096876 Jul 13, 2019 (153)
90 Northern Sweden NC_000016.9 - 31096876 Jul 13, 2019 (153)
91 TopMed NC_000016.10 - 31085555 Oct 12, 2018 (152)
92 UK 10K study - Twins NC_000016.9 - 31096876 Oct 12, 2018 (152)
93 A Vietnamese Genetic Variation Database NC_000016.9 - 31096876 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)
rs58259211 May 24, 2008 (130)
rs386593265 Aug 21, 2014 (142)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss77131322, ss84200086, ss109298601, ss115026844, ss118236112, ss168117777, ss169573610, ss171172263, ss201611258, ss207622104, ss255620513, ss291944762, ss480952377, ss1696466949, ss1713536018, ss2094890056, ss3643103526 NC_000016.8:31004376:A:C NC_000016.10:31085554:A:C (self)
69132092, 38370208, 27147072, 188665089, 14750657, 38370208, 8518743, ss227214741, ss237004889, ss243348934, ss480972148, ss481940478, ss485271116, ss537238627, ss564870493, ss660625280, ss778908986, ss783081486, ss784039100, ss832339824, ss834370319, ss992432542, ss1080589001, ss1355977116, ss1427823799, ss1577894818, ss1634304693, ss1677298726, ss1752190345, ss1808488882, ss1935857447, ss1968250975, ss2028715702, ss2095066077, ss2157129948, ss2376533899, ss2633311800, ss2701637526, ss2942118930, ss2985066748, ss3014335102, ss3351408481, ss3627511056, ss3631298611, ss3633825125, ss3634639898, ss3635513469, ss3636330221, ss3637264895, ss3638122201, ss3640347217, ss3641070960, ss3641366445, ss3652107619, ss3681408824, ss3741465792, ss3744431309, ss3744940326, ss3753863620, ss3772438628 NC_000016.9:31096875:A:C NC_000016.10:31085554:A:C (self)
142684377, ss2211737687, ss3028180738, ss3244230971, ss3699138460, ss3819156684 NC_000016.10:31085554:A:C NC_000016.10:31085554:A:C (self)
ss6003349, ss43969109, ss74963683, ss103290718, ss119477699, ss160681541, ss161771435, ss173738367 NT_010393.16:31036875:A:C NC_000016.10:31085554:A:C (self)
ss17564152, ss19344962 NT_024812.10:2496542:A:C NC_000016.10:31085554:A:C (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 rs4468641

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.post308+0fe9b3b