Name: rs4696688
Published: September 21, 2022
License: Open Access

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.

rs4696688

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:7938188 (GRCh38.p14) 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: C=0.116755 (30904/264690, TOPMED)
C=0.103178 (14421/139768, GnomAD)
G=0.47526 (13430/28258, 14KJPN) (+ 17 more)
G=0.47530 (7966/16760, 8.3KJPN)
C=0.08988 (1402/15598, ALFA)
C=0.1879 (1203/6404, 1000G_30x)
C=0.1943 (973/5008, 1000G)
C=0.0935 (412/4406, Estonian)
C=0.0784 (302/3854, ALSPAC)
C=0.0755 (280/3708, TWINSUK)
G=0.4696 (1376/2930, KOREAN)
C=0.083 (83/998, GoNL)
G=0.469 (369/786, PRJEB37584)
C=0.088 (53/600, NorthernSweden)
C=0.202 (65/322, HapMap)
G=0.431 (94/218, SGDP_PRJ)
C=0.074 (16/216, Qatari)
C=0.440 (95/216, Vietnamese)
C=0.07 (3/40, GENOME_DK)
G=0.43 (12/28, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: AFAP1 : Intron Variant
LOC389199 : 2KB Upstream Variant
Publications: 0 citations
Genomic View: See rs on genome

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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	15598	G=0.91012	C=0.08988	0.82985	0.009617	0.160533	2
European	Sub	10974	G=0.91471	C=0.08529	0.836158	0.006743	0.157099	0
African	Sub	2946	G=0.9358	C=0.0642	0.875764	0.004073	0.120163	0
African Others	Sub	114	G=0.895	C=0.105	0.789474	0.0	0.210526	0
African American	Sub	2832	G=0.9375	C=0.0625	0.879237	0.004237	0.116525	0
Asian	Sub	112	G=0.527	C=0.473	0.25	0.196429	0.553571	0
East Asian	Sub	86	G=0.48	C=0.52	0.186047	0.232558	0.581395	1
Other Asian	Sub	26	G=0.69	C=0.31	0.461538	0.076923	0.461538	0
Latin American 1	Sub	146	G=0.911	C=0.089	0.835616	0.013699	0.150685	0
Latin American 2	Sub	610	G=0.816	C=0.184	0.672131	0.039344	0.288525	0
South Asian	Sub	98	G=0.82	C=0.18	0.714286	0.081633	0.204082	3
Other	Sub	712	G=0.886	C=0.114	0.783708	0.011236	0.205056	0

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").

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Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.883245	C=0.116755
gnomAD - Genomes	Global	Study-wide	139768	G=0.896822	C=0.103178
gnomAD - Genomes	European	Sub	75554	G=0.90763	C=0.09237
gnomAD - Genomes	African	Sub	41992	G=0.93368	C=0.06632
gnomAD - Genomes	American	Sub	13642	G=0.82143	C=0.17857
gnomAD - Genomes	Ashkenazi Jewish	Sub	3318	G=0.8909	C=0.1091
gnomAD - Genomes	East Asian	Sub	3118	G=0.4971	C=0.5029
gnomAD - Genomes	Other	Sub	2144	G=0.8643	C=0.1357
14KJPN	JAPANESE	Study-wide	28258	G=0.47526	C=0.52474
8.3KJPN	JAPANESE	Study-wide	16760	G=0.47530	C=0.52470
Allele Frequency Aggregator	Total	Global	15598	G=0.91012	C=0.08988
Allele Frequency Aggregator	European	Sub	10974	G=0.91471	C=0.08529
Allele Frequency Aggregator	African	Sub	2946	G=0.9358	C=0.0642
Allele Frequency Aggregator	Other	Sub	712	G=0.886	C=0.114
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.816	C=0.184
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.911	C=0.089
Allele Frequency Aggregator	Asian	Sub	112	G=0.527	C=0.473
Allele Frequency Aggregator	South Asian	Sub	98	G=0.82	C=0.18
1000Genomes_30x	Global	Study-wide	6404	G=0.8121	C=0.1879
1000Genomes_30x	African	Sub	1786	G=0.9267	C=0.0733
1000Genomes_30x	Europe	Sub	1266	G=0.9226	C=0.0774
1000Genomes_30x	South Asian	Sub	1202	G=0.7962	C=0.2038
1000Genomes_30x	East Asian	Sub	1170	G=0.5162	C=0.4838
1000Genomes_30x	American	Sub	980	G=0.834	C=0.166
1000Genomes	Global	Study-wide	5008	G=0.8057	C=0.1943
1000Genomes	African	Sub	1322	G=0.9274	C=0.0726
1000Genomes	East Asian	Sub	1008	G=0.5188	C=0.4812
1000Genomes	Europe	Sub	1006	G=0.9225	C=0.0775
1000Genomes	South Asian	Sub	978	G=0.798	C=0.202
1000Genomes	American	Sub	694	G=0.833	C=0.167
Genetic variation in the Estonian population	Estonian	Study-wide	4406	G=0.9065	C=0.0935
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.9216	C=0.0784
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.9245	C=0.0755
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.4696	A=0.0000, C=0.5304
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.917	C=0.083
CNV burdens in cranial meningiomas	Global	Study-wide	786	G=0.469	C=0.531
CNV burdens in cranial meningiomas	CRM	Sub	786	G=0.469	C=0.531
Northern Sweden	ACPOP	Study-wide	600	G=0.912	C=0.088
HapMap	Global	Study-wide	322	G=0.798	C=0.202
HapMap	African	Sub	118	G=0.864	C=0.136
HapMap	American	Sub	116	G=0.914	C=0.086
HapMap	Asian	Sub	88	G=0.56	C=0.44
SGDP_PRJ	Global	Study-wide	218	G=0.431	C=0.569
Qatari	Global	Study-wide	216	G=0.926	C=0.074
A Vietnamese Genetic Variation Database	Global	Study-wide	216	G=0.560	C=0.440
The Danish reference pan genome	Danish	Study-wide	40	G=0.93	C=0.07
Siberian	Global	Study-wide	28	G=0.43	C=0.57

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.p14 chr 4	NC_000004.12:g.7938188G>A
GRCh38.p14 chr 4	NC_000004.12:g.7938188G>C
GRCh37.p13 chr 4	NC_000004.11:g.7939915G>A
GRCh37.p13 chr 4	NC_000004.11:g.7939915G>C

Gene: AFAP1, actin filament associated protein 1 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
AFAP1 transcript variant A	NM_001134647.2:c.-3+1468C… NM_001134647.2:c.-3+1468C>T	N/A	Intron Variant
AFAP1 transcript variant 4	NM_001371091.1:c.-781+146… NM_001371091.1:c.-781+1468C>T	N/A	Intron Variant
AFAP1 transcript variant 2	NM_198595.3:c.-3+1468C>T	N/A	Intron Variant
AFAP1 transcript variant 3	NM_001371090.1:c.	N/A	Genic Upstream Transcript Variant
AFAP1 transcript variant X3	XM_006713909.4:c.61+404C>T	N/A	Intron Variant
AFAP1 transcript variant X1	XM_011513544.4:c.	N/A	Genic Upstream Transcript Variant
AFAP1 transcript variant X2	XM_017008535.2:c.	N/A	Genic Upstream Transcript Variant
AFAP1 transcript variant X5	XM_017008536.1:c.	N/A	Genic Upstream Transcript Variant
AFAP1 transcript variant X4	XM_047416061.1:c.	N/A	Genic Upstream Transcript Variant

Gene: LOC389199, uncharacterized LOC389199 (plus strand) : 2KB Upstream Variant

Molecule type	Change	Amino acid[Codon]	SO Term
LOC389199 transcript	NR_172651.1:n.	N/A	Upstream Transcript Variant

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

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.p14 chr 4	NC_000004.12:g.7938188=	NC_000004.12:g.7938188G>A	NC_000004.12:g.7938188G>C
GRCh37.p13 chr 4	NC_000004.11:g.7939915=	NC_000004.11:g.7939915G>A	NC_000004.11:g.7939915G>C
AFAP1 transcript variant A	NM_001134647.1:c.-3+1468=	NM_001134647.1:c.-3+1468C>T	NM_001134647.1:c.-3+1468C>G
AFAP1 transcript variant A	NM_001134647.2:c.-3+1468=	NM_001134647.2:c.-3+1468C>T	NM_001134647.2:c.-3+1468C>G
AFAP1 transcript variant 4	NM_001371091.1:c.-781+1468=	NM_001371091.1:c.-781+1468C>T	NM_001371091.1:c.-781+1468C>G
AFAP1 transcript variant 2	NM_198595.2:c.-3+1468=	NM_198595.2:c.-3+1468C>T	NM_198595.2:c.-3+1468C>G
AFAP1 transcript variant 2	NM_198595.3:c.-3+1468=	NM_198595.3:c.-3+1468C>T	NM_198595.3:c.-3+1468C>G
AFAP1 transcript variant X3	XM_005247993.1:c.-3+1468=	XM_005247993.1:c.-3+1468C>T	XM_005247993.1:c.-3+1468C>G
AFAP1 transcript variant X3	XM_006713909.4:c.61+404=	XM_006713909.4:c.61+404C>T	XM_006713909.4:c.61+404C>G

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#.

62 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	WI_SSAHASNP	ss6468892	Feb 20, 2003 (111)
2	BCM_SSAHASNP	ss10108905	Jul 11, 2003 (116)
3	ILLUMINA	ss65760531	Oct 16, 2006 (127)
4	BGI	ss104038281	Dec 01, 2009 (131)
5	1000GENOMES	ss111748157	Jan 25, 2009 (130)
6	GMI	ss156831003	Dec 01, 2009 (131)
7	ILLUMINA	ss160699609	Dec 01, 2009 (131)
8	COMPLETE_GENOMICS	ss163065120	Jul 04, 2010 (132)
9	1000GENOMES	ss220729022	Jul 14, 2010 (132)
10	1000GENOMES	ss232249949	Jul 14, 2010 (132)
11	1000GENOMES	ss239573542	Jul 15, 2010 (132)
12	GMI	ss277564790	May 04, 2012 (137)
13	ILLUMINA	ss482012722	Sep 08, 2015 (146)
14	ILLUMINA	ss533161121	Sep 08, 2015 (146)
15	TISHKOFF	ss557294030	Apr 25, 2013 (138)
16	SSMP	ss651050321	Apr 25, 2013 (138)
17	EVA-GONL	ss979733974	Aug 21, 2014 (142)
18	JMKIDD_LAB	ss1071256190	Aug 21, 2014 (142)
19	1000GENOMES	ss1308320069	Aug 21, 2014 (142)
20	DDI	ss1429763035	Apr 01, 2015 (144)
21	EVA_GENOME_DK	ss1580403489	Apr 01, 2015 (144)
22	EVA_DECODE	ss1589228376	Apr 01, 2015 (144)
23	EVA_UK10K_ALSPAC	ss1609353049	Apr 01, 2015 (144)
24	EVA_UK10K_TWINSUK	ss1652347082	Apr 01, 2015 (144)
25	WEILL_CORNELL_DGM	ss1922970911	Feb 12, 2016 (147)
26	GENOMED	ss1969651498	Sep 14, 2016 (149)
27	JJLAB	ss2022058119	Sep 14, 2016 (149)
28	USC_VALOUEV	ss2150168923	Dec 20, 2016 (150)
29	HUMAN_LONGEVITY	ss2260249968	Dec 20, 2016 (150)
30	SYSTEMSBIOZJU	ss2625530923	Nov 08, 2017 (151)
31	GRF	ss2705606554	Nov 08, 2017 (151)
32	GNOMAD	ss2805325033	Nov 08, 2017 (151)
33	ILLUMINA	ss3022344857	Nov 08, 2017 (151)
34	BIOINF_KMB_FNS_UNIBA	ss3024799029	Nov 08, 2017 (151)
35	CSHL	ss3345529812	Nov 08, 2017 (151)
36	ILLUMINA	ss3628897304	Oct 12, 2018 (152)
37	ILLUMINA	ss3636638815	Oct 12, 2018 (152)
38	ILLUMINA	ss3652827681	Oct 12, 2018 (152)
39	EGCUT_WGS	ss3662016984	Jul 13, 2019 (153)
40	EVA_DECODE	ss3711352312	Jul 13, 2019 (153)
41	ILLUMINA	ss3726107748	Jul 13, 2019 (153)
42	ACPOP	ss3730829971	Jul 13, 2019 (153)
43	EVA	ss3761360447	Jul 13, 2019 (153)
44	KHV_HUMAN_GENOMES	ss3804498228	Jul 13, 2019 (153)
45	EVA	ss3828357460	Apr 25, 2020 (154)
46	SGDP_PRJ	ss3858155347	Apr 25, 2020 (154)
47	KRGDB	ss3904295802	Apr 25, 2020 (154)
48	EVA	ss3984523236	Apr 26, 2021 (155)
49	TOPMED	ss4601990824	Apr 26, 2021 (155)
50	TOMMO_GENOMICS	ss5164079176	Apr 26, 2021 (155)
51	1000G_HIGH_COVERAGE	ss5257948545	Oct 17, 2022 (156)
52	EVA	ss5346740591	Oct 17, 2022 (156)
53	HUGCELL_USP	ss5456871576	Oct 17, 2022 (156)
54	EVA	ss5507380120	Oct 17, 2022 (156)
55	1000G_HIGH_COVERAGE	ss5538338073	Oct 17, 2022 (156)
56	SANFORD_IMAGENETICS	ss5634292807	Oct 17, 2022 (156)
57	TOMMO_GENOMICS	ss5697693946	Oct 17, 2022 (156)
58	YY_MCH	ss5804730831	Oct 17, 2022 (156)
59	EVA	ss5843514367	Oct 17, 2022 (156)
60	EVA	ss5854069530	Oct 17, 2022 (156)
61	EVA	ss5862043820	Oct 17, 2022 (156)
62	EVA	ss5962666992	Oct 17, 2022 (156)
63	1000Genomes	NC_000004.11 - 7939915	Oct 12, 2018 (152)
64	1000Genomes_30x	NC_000004.12 - 7938188	Oct 17, 2022 (156)
65	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 7939915	Oct 12, 2018 (152)
66	Genetic variation in the Estonian population	NC_000004.11 - 7939915	Oct 12, 2018 (152)
67	The Danish reference pan genome	NC_000004.11 - 7939915	Apr 25, 2020 (154)
68	gnomAD - Genomes	NC_000004.12 - 7938188	Apr 26, 2021 (155)
69	Genome of the Netherlands Release 5	NC_000004.11 - 7939915	Apr 25, 2020 (154)
70	HapMap	NC_000004.12 - 7938188	Apr 25, 2020 (154)
71	KOREAN population from KRGDB	NC_000004.11 - 7939915	Apr 25, 2020 (154)
72	Northern Sweden	NC_000004.11 - 7939915	Jul 13, 2019 (153)
73	CNV burdens in cranial meningiomas	NC_000004.11 - 7939915	Apr 26, 2021 (155)
74	Qatari	NC_000004.11 - 7939915	Apr 25, 2020 (154)
75	SGDP_PRJ	NC_000004.11 - 7939915	Apr 25, 2020 (154)
76	Siberian	NC_000004.11 - 7939915	Apr 25, 2020 (154)
77	8.3KJPN	NC_000004.11 - 7939915	Apr 26, 2021 (155)
78	14KJPN	NC_000004.12 - 7938188	Oct 17, 2022 (156)
79	TopMed	NC_000004.12 - 7938188	Apr 26, 2021 (155)
80	UK 10K study - Twins	NC_000004.11 - 7939915	Oct 12, 2018 (152)
81	A Vietnamese Genetic Variation Database	NC_000004.11 - 7939915	Jul 13, 2019 (153)
82	ALFA	NC_000004.12 - 7938188	Apr 26, 2021 (155)

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
11473196, ss3904295802	NC_000004.11:7939914:G:A	NC_000004.12:7938187:G:A	(self)
ss111748157, ss163065120, ss277564790, ss1589228376	NC_000004.10:7990814:G:C	NC_000004.12:7938187:G:C	(self)
19665082, 10955606, 7755232, 6568428, 4816970, 11473196, 4114836, 72595, 5012841, 10172327, 2685277, 22048483, 10955606, 2394271, ss220729022, ss232249949, ss239573542, ss482012722, ss533161121, ss557294030, ss651050321, ss979733974, ss1071256190, ss1308320069, ss1429763035, ss1580403489, ss1609353049, ss1652347082, ss1922970911, ss1969651498, ss2022058119, ss2150168923, ss2625530923, ss2705606554, ss2805325033, ss3022344857, ss3345529812, ss3628897304, ss3636638815, ss3652827681, ss3662016984, ss3730829971, ss3761360447, ss3828357460, ss3858155347, ss3904295802, ss3984523236, ss5164079176, ss5346740591, ss5507380120, ss5634292807, ss5843514367, ss5962666992	NC_000004.11:7939914:G:C	NC_000004.12:7938187:G:C	(self)
25864008, 139482949, 2551921, 31531050, 439368380, 9571020502, ss2260249968, ss3024799029, ss3711352312, ss3726107748, ss3804498228, ss4601990824, ss5257948545, ss5456871576, ss5538338073, ss5697693946, ss5804730831, ss5854069530, ss5862043820	NC_000004.12:7938187:G:C	NC_000004.12:7938187:G:C	(self)
ss6468892, ss65760531, ss104038281, ss156831003, ss160699609	NT_006051.18:6461268:G:C	NC_000004.12:7938187:G:C	(self)
ss10108905	NT_006307.14:53382:G:C	NC_000004.12:7938187:G:C	(self)

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs4696688

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.

Choose placement

dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs4696688