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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.

rs921987

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr7:151236197 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.402354 (106499/264690, TOPMED)
A=0.401791 (56270/140048, GnomAD)
A=0.40807 (25139/61604, ALFA) (+ 16 more)
G=0.29478 (4940/16758, 8.3KJPN)
A=0.4485 (2246/5008, 1000G)
A=0.4313 (1932/4480, Estonian)
A=0.3967 (1529/3854, ALSPAC)
A=0.4167 (1545/3708, TWINSUK)
G=0.2498 (732/2930, KOREAN)
G=0.2620 (480/1832, Korea1K)
A=0.368 (367/998, GoNL)
A=0.413 (248/600, NorthernSweden)
A=0.109 (58/534, MGP)
G=0.314 (115/366, SGDP_PRJ)
A=0.324 (70/216, Qatari)
G=0.255 (54/212, Vietnamese)
A=0.268 (30/112, HapMap)
G=0.30 (13/44, Siberian)
A=0.30 (12/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
CHPF2 : 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 7 NC_000007.14:g.151236197G>A
GRCh38.p13 chr 7 NC_000007.14:g.151236197G>C
GRCh37.p13 chr 7 NC_000007.13:g.150933283G>A
GRCh37.p13 chr 7 NC_000007.13:g.150933283G>C
Gene: CHPF2, chondroitin polymerizing factor 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
CHPF2 transcript variant 2 NM_001284295.2:c.805-211G…

NM_001284295.2:c.805-211G>A

N/A Intron Variant
CHPF2 transcript variant 3 NM_001389651.1:c.828+585G…

NM_001389651.1:c.828+585G>A

N/A Intron Variant
CHPF2 transcript variant 4 NM_001389652.1:c.616-211G…

NM_001389652.1:c.616-211G>A

N/A Intron Variant
CHPF2 transcript variant 5 NM_001389653.1:c.615+585G…

NM_001389653.1:c.615+585G>A

N/A Intron Variant
CHPF2 transcript variant 1 NM_019015.3:c.829-211G>A N/A Intron Variant
CHPF2 transcript variant 6 NR_171547.1:n. N/A Intron Variant
CHPF2 transcript variant 7 NR_171548.1:n. N/A Intron Variant
CHPF2 transcript variant 8 NR_171549.1: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.

Not Reported in ClinVar

ALFA Allele Frequency (New)
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 61604 G=0.59193 A=0.40807
European Sub 46726 G=0.59034 A=0.40966
African Sub 3958 G=0.6668 A=0.3332
African Others Sub 152 G=0.678 A=0.322
African American Sub 3806 G=0.6663 A=0.3337
Asian Sub 446 G=0.287 A=0.713
East Asian Sub 378 G=0.278 A=0.722
Other Asian Sub 68 G=0.34 A=0.66
Latin American 1 Sub 356 G=0.657 A=0.343
Latin American 2 Sub 5418 G=0.5779 A=0.4221
South Asian Sub 170 G=0.571 A=0.429
Other Sub 4530 G=0.5854 A=0.4146


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 G=0.597646 A=0.402354
gnomAD - Genomes Global Study-wide 140048 G=0.598209 A=0.401791
gnomAD - Genomes European Sub 75842 G=0.58515 A=0.41485
gnomAD - Genomes African Sub 41962 G=0.66379 A=0.33621
gnomAD - Genomes American Sub 13644 G=0.54845 A=0.45155
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.5927 A=0.4073
gnomAD - Genomes East Asian Sub 3124 G=0.2859 A=0.7141
gnomAD - Genomes Other Sub 2152 G=0.5572 A=0.4428
8.3KJPN JAPANESE Study-wide 16758 G=0.29478 A=0.70522
1000Genomes Global Study-wide 5008 G=0.5515 A=0.4485
1000Genomes African Sub 1322 G=0.6785 A=0.3215
1000Genomes East Asian Sub 1008 G=0.2817 A=0.7183
1000Genomes Europe Sub 1006 G=0.5507 A=0.4493
1000Genomes South Asian Sub 978 G=0.639 A=0.361
1000Genomes American Sub 694 G=0.579 A=0.421
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.5687 A=0.4313
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.6033 A=0.3967
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.5833 A=0.4167
KOREAN population from KRGDB KOREAN Study-wide 2930 G=0.2498 A=0.7502, C=0.0000
Korean Genome Project KOREAN Study-wide 1832 G=0.2620 A=0.7380
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.632 A=0.368
Northern Sweden ACPOP Study-wide 600 G=0.587 A=0.413
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.891 A=0.109
SGDP_PRJ Global Study-wide 366 G=0.314 A=0.686
Qatari Global Study-wide 216 G=0.676 A=0.324
A Vietnamese Genetic Variation Database Global Study-wide 212 G=0.255 A=0.745
HapMap Global Study-wide 112 G=0.732 A=0.268
HapMap African Sub 112 G=0.732 A=0.268
Siberian Global Study-wide 44 G=0.30 A=0.70
The Danish reference pan genome Danish Study-wide 40 G=0.70 A=0.30
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 G= A C
GRCh38.p13 chr 7 NC_000007.14:g.151236197= NC_000007.14:g.151236197G>A NC_000007.14:g.151236197G>C
GRCh37.p13 chr 7 NC_000007.13:g.150933283= NC_000007.13:g.150933283G>A NC_000007.13:g.150933283G>C
CHPF2 transcript variant 2 NM_001284295.2:c.805-211= NM_001284295.2:c.805-211G>A NM_001284295.2:c.805-211G>C
CHPF2 transcript variant 3 NM_001389651.1:c.828+585= NM_001389651.1:c.828+585G>A NM_001389651.1:c.828+585G>C
CHPF2 transcript variant 4 NM_001389652.1:c.616-211= NM_001389652.1:c.616-211G>A NM_001389652.1:c.616-211G>C
CHPF2 transcript variant 5 NM_001389653.1:c.615+585= NM_001389653.1:c.615+585G>A NM_001389653.1:c.615+585G>C
CHPF2 transcript NM_019015.1:c.829-211= NM_019015.1:c.829-211G>A NM_019015.1:c.829-211G>C
CHPF2 transcript variant 1 NM_019015.3:c.829-211= NM_019015.3:c.829-211G>A NM_019015.3:c.829-211G>C
CHPF2 transcript variant X1 XM_005250014.1:c.805-211= XM_005250014.1:c.805-211G>A XM_005250014.1:c.805-211G>C
CHPF2 transcript variant X2 XM_005250015.1:c.828+585= XM_005250015.1:c.828+585G>A XM_005250015.1:c.828+585G>C
CHPF2 transcript variant X3 XM_005250016.1:c.829-211= XM_005250016.1:c.829-211G>A XM_005250016.1:c.829-211G>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#.

79 SubSNP, 19 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss1358662 Oct 05, 2000 (86)
2 SC_JCM ss3428749 Sep 28, 2001 (100)
3 SC_JCM ss5790983 Feb 20, 2003 (111)
4 WI_SSAHASNP ss6513430 Feb 20, 2003 (111)
5 BCM_SSAHASNP ss10363841 Jul 11, 2003 (116)
6 WI_SSAHASNP ss11855759 Jul 11, 2003 (116)
7 CSHL-HAPMAP ss17920936 Feb 27, 2004 (120)
8 ABI ss42974046 Mar 14, 2006 (126)
9 BCMHGSC_JDW ss93791638 Mar 25, 2008 (129)
10 BGI ss105582486 Feb 03, 2009 (130)
11 1000GENOMES ss114654560 Jan 25, 2009 (130)
12 ILLUMINA ss152536339 Dec 01, 2009 (131)
13 ILLUMINA ss159102624 Dec 01, 2009 (131)
14 ILLUMINA ss159846001 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss165685564 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss167260808 Jul 04, 2010 (132)
17 ILLUMINA ss168870783 Jul 04, 2010 (132)
18 BUSHMAN ss198491088 Jul 04, 2010 (132)
19 1000GENOMES ss223414511 Jul 14, 2010 (132)
20 1000GENOMES ss234225944 Jul 15, 2010 (132)
21 1000GENOMES ss241125192 Jul 15, 2010 (132)
22 GMI ss279589469 May 04, 2012 (137)
23 ILLUMINA ss479154437 Sep 08, 2015 (146)
24 ILLUMINA ss479863556 May 04, 2012 (137)
25 ILLUMINA ss485378069 May 04, 2012 (137)
26 ILLUMINA ss533344705 Sep 08, 2015 (146)
27 TISHKOFF ss560400517 Apr 25, 2013 (138)
28 SSMP ss654814443 Apr 25, 2013 (138)
29 ILLUMINA ss779666050 Sep 08, 2015 (146)
30 ILLUMINA ss781087539 Sep 08, 2015 (146)
31 ILLUMINA ss832615420 Jul 13, 2019 (153)
32 ILLUMINA ss835139439 Sep 08, 2015 (146)
33 EVA-GONL ss984960277 Aug 21, 2014 (142)
34 JMKIDD_LAB ss1075101291 Aug 21, 2014 (142)
35 1000GENOMES ss1327749431 Aug 21, 2014 (142)
36 DDI ss1431330038 Apr 01, 2015 (144)
37 EVA_GENOME_DK ss1582463946 Apr 01, 2015 (144)
38 EVA_DECODE ss1594550867 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1619537584 Apr 01, 2015 (144)
40 EVA_UK10K_TWINSUK ss1662531617 Apr 01, 2015 (144)
41 EVA_MGP ss1711186552 Apr 01, 2015 (144)
42 HAMMER_LAB ss1805293828 Sep 08, 2015 (146)
43 WEILL_CORNELL_DGM ss1928223203 Feb 12, 2016 (147)
44 GENOMED ss1970852025 Jul 19, 2016 (147)
45 JJLAB ss2024800647 Sep 14, 2016 (149)
46 USC_VALOUEV ss2153024456 Dec 20, 2016 (150)
47 HUMAN_LONGEVITY ss2299083173 Dec 20, 2016 (150)
48 TOPMED ss2468628542 Dec 20, 2016 (150)
49 SYSTEMSBIOZJU ss2626885333 Nov 08, 2017 (151)
50 ILLUMINA ss2634679134 Nov 08, 2017 (151)
51 GRF ss2708751899 Nov 08, 2017 (151)
52 GNOMAD ss2860874930 Nov 08, 2017 (151)
53 AFFY ss2986055938 Nov 08, 2017 (151)
54 SWEGEN ss3002298806 Nov 08, 2017 (151)
55 BIOINF_KMB_FNS_UNIBA ss3026189286 Nov 08, 2017 (151)
56 CSHL ss3347918330 Nov 08, 2017 (151)
57 TOPMED ss3548481067 Nov 08, 2017 (151)
58 ILLUMINA ss3629948124 Oct 12, 2018 (152)
59 ILLUMINA ss3632582349 Oct 12, 2018 (152)
60 ILLUMINA ss3636883849 Oct 12, 2018 (152)
61 ILLUMINA ss3638732486 Oct 12, 2018 (152)
62 ILLUMINA ss3642597974 Oct 12, 2018 (152)
63 ILLUMINA ss3654187137 Oct 12, 2018 (152)
64 EGCUT_WGS ss3670037892 Jul 13, 2019 (153)
65 EVA_DECODE ss3720996950 Jul 13, 2019 (153)
66 ACPOP ss3735204618 Jul 13, 2019 (153)
67 EVA ss3767346785 Jul 13, 2019 (153)
68 PACBIO ss3786002841 Jul 13, 2019 (153)
69 PACBIO ss3791274686 Jul 13, 2019 (153)
70 PACBIO ss3796154995 Jul 13, 2019 (153)
71 KHV_HUMAN_GENOMES ss3810515269 Jul 13, 2019 (153)
72 EVA ss3830898443 Apr 26, 2020 (154)
73 EVA ss3838949654 Apr 26, 2020 (154)
74 EVA ss3844407242 Apr 26, 2020 (154)
75 SGDP_PRJ ss3868729155 Apr 26, 2020 (154)
76 KRGDB ss3916122350 Apr 26, 2020 (154)
77 KOGIC ss3962878981 Apr 26, 2020 (154)
78 TOPMED ss4769051951 Apr 26, 2021 (155)
79 TOMMO_GENOMICS ss5186294080 Apr 26, 2021 (155)
80 1000Genomes NC_000007.13 - 150933283 Oct 12, 2018 (152)
81 The Avon Longitudinal Study of Parents and Children NC_000007.13 - 150933283 Oct 12, 2018 (152)
82 Genetic variation in the Estonian population NC_000007.13 - 150933283 Oct 12, 2018 (152)
83 The Danish reference pan genome NC_000007.13 - 150933283 Apr 26, 2020 (154)
84 gnomAD - Genomes NC_000007.14 - 151236197 Apr 26, 2021 (155)
85 Genome of the Netherlands Release 5 NC_000007.13 - 150933283 Apr 26, 2020 (154)
86 HapMap NC_000007.14 - 151236197 Apr 26, 2020 (154)
87 KOREAN population from KRGDB NC_000007.13 - 150933283 Apr 26, 2020 (154)
88 Korean Genome Project NC_000007.14 - 151236197 Apr 26, 2020 (154)
89 Medical Genome Project healthy controls from Spanish population NC_000007.13 - 150933283 Apr 26, 2020 (154)
90 Northern Sweden NC_000007.13 - 150933283 Jul 13, 2019 (153)
91 Qatari NC_000007.13 - 150933283 Apr 26, 2020 (154)
92 SGDP_PRJ NC_000007.13 - 150933283 Apr 26, 2020 (154)
93 Siberian NC_000007.13 - 150933283 Apr 26, 2020 (154)
94 8.3KJPN NC_000007.13 - 150933283 Apr 26, 2021 (155)
95 TopMed NC_000007.14 - 151236197 Apr 26, 2021 (155)
96 UK 10K study - Twins NC_000007.13 - 150933283 Oct 12, 2018 (152)
97 A Vietnamese Genetic Variation Database NC_000007.13 - 150933283 Jul 13, 2019 (153)
98 ALFA NC_000007.14 - 151236197 Apr 26, 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).

Associated ID History Updated (Build)
rs118020893 Aug 16, 2010 (132)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss93791638, ss114654560, ss165685564, ss167260808, ss198491088, ss279589469, ss485378069, ss1594550867 NC_000007.12:150564215:G:A NC_000007.14:151236196:G:A (self)
39815754, 22155632, 15776140, 8628884, 9885494, 23299744, 302312, 8489483, 10265133, 20746135, 5540810, 44263387, 22155632, 4931396, ss223414511, ss234225944, ss241125192, ss479154437, ss479863556, ss533344705, ss560400517, ss654814443, ss779666050, ss781087539, ss832615420, ss835139439, ss984960277, ss1075101291, ss1327749431, ss1431330038, ss1582463946, ss1619537584, ss1662531617, ss1711186552, ss1805293828, ss1928223203, ss1970852025, ss2024800647, ss2153024456, ss2468628542, ss2626885333, ss2634679134, ss2708751899, ss2860874930, ss2986055938, ss3002298806, ss3347918330, ss3629948124, ss3632582349, ss3636883849, ss3638732486, ss3642597974, ss3654187137, ss3670037892, ss3735204618, ss3767346785, ss3786002841, ss3791274686, ss3796154995, ss3830898443, ss3838949654, ss3868729155, ss3916122350, ss5186294080 NC_000007.13:150933282:G:A NC_000007.14:151236196:G:A (self)
281144273, 3523667, 19256982, 379168009, 606429510, 11900370387, ss2299083173, ss3026189286, ss3548481067, ss3720996950, ss3810515269, ss3844407242, ss3962878981, ss4769051951 NC_000007.14:151236196:G:A NC_000007.14:151236196:G:A (self)
ss10363841, ss11855759 NT_007914.12:11476053:G:A NC_000007.14:151236196:G:A (self)
ss17920936 NT_007914.13:11509298:G:A NC_000007.14:151236196:G:A (self)
ss1358662, ss3428749, ss5790983, ss6513430, ss42974046, ss105582486, ss152536339, ss159102624, ss159846001, ss168870783 NT_007914.15:11528905:G:A NC_000007.14:151236196:G:A (self)
ss198491088 NC_000007.12:150564215:G:C NC_000007.14:151236196:G:C (self)
23299744, ss3916122350 NC_000007.13:150933282:G:C NC_000007.14:151236196:G: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 rs921987

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