Name: rs4555615
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.

rs4555615

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr4:7937851 (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>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.281541 (74521/264690, TOPMED)
A=0.262707 (36780/140004, GnomAD)
G=0.22836 (6453/28258, 14KJPN) (+ 16 more)
A=0.21816 (4121/18890, ALFA)
G=0.22649 (3796/16760, 8.3KJPN)
A=0.4083 (2615/6404, 1000G_30x)
A=0.4141 (2074/5008, 1000G)
A=0.2118 (949/4480, Estonian)
A=0.1565 (603/3854, ALSPAC)
A=0.1548 (574/3708, TWINSUK)
G=0.2130 (624/2930, KOREAN)
G=0.2260 (414/1832, Korea1K)
A=0.168 (168/998, GoNL)
A=0.192 (115/600, NorthernSweden)
G=0.345 (122/354, SGDP_PRJ)
A=0.227 (49/216, Qatari)
G=0.324 (68/210, Vietnamese)
G=0.32 (14/44, Siberian)
A=0.12 (5/40, GENOME_DK)

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	18890	G=0.78184	A=0.21816	0.614293	0.050609	0.335098	2
European	Sub	14286	G=0.81625	A=0.18375	0.665407	0.032899	0.301694	0
African	Sub	2946	G=0.6806	A=0.3194	0.450781	0.089613	0.459606	3
African Others	Sub	114	G=0.649	A=0.351	0.368421	0.070175	0.561404	2
African American	Sub	2832	G=0.6819	A=0.3181	0.454096	0.090395	0.455508	2
Asian	Sub	112	G=0.232	A=0.768	0.053571	0.589286	0.357143	0
East Asian	Sub	86	G=0.20	A=0.80	0.023256	0.627907	0.348837	0
Other Asian	Sub	26	G=0.35	A=0.65	0.153846	0.461538	0.384615	0
Latin American 1	Sub	146	G=0.795	A=0.205	0.630137	0.041096	0.328767	0
Latin American 2	Sub	610	G=0.634	A=0.366	0.413115	0.144262	0.442623	0
South Asian	Sub	98	G=0.59	A=0.41	0.367347	0.183673	0.44898	0
Other	Sub	692	G=0.746	A=0.254	0.554913	0.063584	0.381503	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").

Download

Study	Population	Group	Sample Size	Ref Allele	Alt Allele
TopMed	Global	Study-wide	264690	G=0.718459	A=0.281541
gnomAD - Genomes	Global	Study-wide	140004	G=0.737293	A=0.262707
gnomAD - Genomes	European	Sub	75830	G=0.81543	A=0.18457
gnomAD - Genomes	African	Sub	41952	G=0.66769	A=0.33231
gnomAD - Genomes	American	Sub	13624	G=0.63117	A=0.36883
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=0.7404	A=0.2596
gnomAD - Genomes	East Asian	Sub	3130	G=0.2537	A=0.7463
gnomAD - Genomes	Other	Sub	2148	G=0.7114	A=0.2886
14KJPN	JAPANESE	Study-wide	28258	G=0.22836	A=0.77164
Allele Frequency Aggregator	Total	Global	18890	G=0.78184	A=0.21816
Allele Frequency Aggregator	European	Sub	14286	G=0.81625	A=0.18375
Allele Frequency Aggregator	African	Sub	2946	G=0.6806	A=0.3194
Allele Frequency Aggregator	Other	Sub	692	G=0.746	A=0.254
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.634	A=0.366
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.795	A=0.205
Allele Frequency Aggregator	Asian	Sub	112	G=0.232	A=0.768
Allele Frequency Aggregator	South Asian	Sub	98	G=0.59	A=0.41
8.3KJPN	JAPANESE	Study-wide	16760	G=0.22649	A=0.77351
1000Genomes_30x	Global	Study-wide	6404	G=0.5917	A=0.4083
1000Genomes_30x	African	Sub	1786	G=0.6159	A=0.3841
1000Genomes_30x	Europe	Sub	1266	G=0.8175	A=0.1825
1000Genomes_30x	South Asian	Sub	1202	G=0.5740	A=0.4260
1000Genomes_30x	East Asian	Sub	1170	G=0.2803	A=0.7197
1000Genomes_30x	American	Sub	980	G=0.649	A=0.351
1000Genomes	Global	Study-wide	5008	G=0.5859	A=0.4141
1000Genomes	African	Sub	1322	G=0.6120	A=0.3880
1000Genomes	East Asian	Sub	1008	G=0.2817	A=0.7183
1000Genomes	Europe	Sub	1006	G=0.8231	A=0.1769
1000Genomes	South Asian	Sub	978	G=0.577	A=0.423
1000Genomes	American	Sub	694	G=0.647	A=0.353
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.7882	A=0.2118
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.8435	A=0.1565
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.8452	A=0.1548
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.2130	A=0.7870, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	G=0.2260	A=0.7740
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.832	A=0.168
Northern Sweden	ACPOP	Study-wide	600	G=0.808	A=0.192
SGDP_PRJ	Global	Study-wide	354	G=0.345	A=0.655
Qatari	Global	Study-wide	216	G=0.773	A=0.227
A Vietnamese Genetic Variation Database	Global	Study-wide	210	G=0.324	A=0.676
Siberian	Global	Study-wide	44	G=0.32	A=0.68
The Danish reference pan genome	Danish	Study-wide	40	G=0.88	A=0.12

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.7937851G>A
GRCh38.p14 chr 4	NC_000004.12:g.7937851G>T
GRCh37.p13 chr 4	NC_000004.11:g.7939578G>A
GRCh37.p13 chr 4	NC_000004.11:g.7939578G>T

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+1805C… NM_001134647.2:c.-3+1805C>T	N/A	Intron Variant
AFAP1 transcript variant 4	NM_001371091.1:c.-781+180… NM_001371091.1:c.-781+1805C>T	N/A	Intron Variant
AFAP1 transcript variant 2	NM_198595.3:c.-3+1805C>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+741C>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	T
GRCh38.p14 chr 4	NC_000004.12:g.7937851=	NC_000004.12:g.7937851G>A	NC_000004.12:g.7937851G>T
GRCh37.p13 chr 4	NC_000004.11:g.7939578=	NC_000004.11:g.7939578G>A	NC_000004.11:g.7939578G>T
AFAP1 transcript variant A	NM_001134647.1:c.-3+1805=	NM_001134647.1:c.-3+1805C>T	NM_001134647.1:c.-3+1805C>A
AFAP1 transcript variant A	NM_001134647.2:c.-3+1805=	NM_001134647.2:c.-3+1805C>T	NM_001134647.2:c.-3+1805C>A
AFAP1 transcript variant 4	NM_001371091.1:c.-781+1805=	NM_001371091.1:c.-781+1805C>T	NM_001371091.1:c.-781+1805C>A
AFAP1 transcript variant 2	NM_198595.2:c.-3+1805=	NM_198595.2:c.-3+1805C>T	NM_198595.2:c.-3+1805C>A
AFAP1 transcript variant 2	NM_198595.3:c.-3+1805=	NM_198595.3:c.-3+1805C>T	NM_198595.3:c.-3+1805C>A
AFAP1 transcript variant X3	XM_005247993.1:c.-3+1805=	XM_005247993.1:c.-3+1805C>T	XM_005247993.1:c.-3+1805C>A
AFAP1 transcript variant X3	XM_006713909.4:c.61+741=	XM_006713909.4:c.61+741C>T	XM_006713909.4:c.61+741C>A

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#.

55 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss6155919	Feb 20, 2003 (111)
2	BCM_SSAHASNP	ss10107744	Jul 11, 2003 (116)
3	BGI	ss105803842	Feb 04, 2009 (130)
4	1000GENOMES	ss111748139	Jan 25, 2009 (130)
5	GMI	ss156830989	Dec 01, 2009 (131)
6	COMPLETE_GENOMICS	ss163065109	Jul 04, 2010 (132)
7	BUSHMAN	ss198000979	Jul 04, 2010 (132)
8	1000GENOMES	ss220729018	Jul 14, 2010 (132)
9	1000GENOMES	ss232249947	Jul 14, 2010 (132)
10	1000GENOMES	ss239573540	Jul 15, 2010 (132)
11	GMI	ss277564788	May 04, 2012 (137)
12	TISHKOFF	ss557294023	Apr 25, 2013 (138)
13	SSMP	ss651050318	Apr 25, 2013 (138)
14	EVA-GONL	ss979733970	Aug 21, 2014 (142)
15	JMKIDD_LAB	ss1071256186	Aug 21, 2014 (142)
16	1000GENOMES	ss1308320055	Aug 21, 2014 (142)
17	DDI	ss1429763033	Apr 01, 2015 (144)
18	EVA_GENOME_DK	ss1580403487	Apr 01, 2015 (144)
19	EVA_DECODE	ss1589228372	Apr 01, 2015 (144)
20	EVA_UK10K_ALSPAC	ss1609353042	Apr 01, 2015 (144)
21	EVA_UK10K_TWINSUK	ss1652347075	Apr 01, 2015 (144)
22	HAMMER_LAB	ss1800983458	Sep 08, 2015 (146)
23	WEILL_CORNELL_DGM	ss1922970908	Feb 12, 2016 (147)
24	GENOMED	ss1969651496	Sep 14, 2016 (149)
25	JJLAB	ss2022058117	Sep 14, 2016 (149)
26	USC_VALOUEV	ss2150168921	Dec 20, 2016 (150)
27	HUMAN_LONGEVITY	ss2260249946	Dec 20, 2016 (150)
28	SYSTEMSBIOZJU	ss2625530921	Nov 08, 2017 (151)
29	GRF	ss2705606551	Nov 08, 2017 (151)
30	GNOMAD	ss2805325005	Nov 08, 2017 (151)
31	SWEGEN	ss2994091225	Nov 08, 2017 (151)
32	BIOINF_KMB_FNS_UNIBA	ss3024799027	Nov 08, 2017 (151)
33	CSHL	ss3345529810	Nov 08, 2017 (151)
34	EGCUT_WGS	ss3662016981	Jul 13, 2019 (153)
35	EVA_DECODE	ss3711352307	Jul 13, 2019 (153)
36	ACPOP	ss3730829968	Jul 13, 2019 (153)
37	EVA	ss3761360442	Jul 13, 2019 (153)
38	KHV_HUMAN_GENOMES	ss3804498223	Jul 13, 2019 (153)
39	EVA	ss3828357458	Apr 25, 2020 (154)
40	SGDP_PRJ	ss3858155340	Apr 25, 2020 (154)
41	KRGDB	ss3904295795	Apr 25, 2020 (154)
42	KOGIC	ss3953476527	Apr 25, 2020 (154)
43	TOPMED	ss4601990713	Apr 26, 2021 (155)
44	TOMMO_GENOMICS	ss5164079157	Apr 26, 2021 (155)
45	1000G_HIGH_COVERAGE	ss5257948532	Oct 17, 2022 (156)
46	HUGCELL_USP	ss5456871566	Oct 17, 2022 (156)
47	EVA	ss5507380119	Oct 17, 2022 (156)
48	1000G_HIGH_COVERAGE	ss5538338055	Oct 17, 2022 (156)
49	SANFORD_IMAGENETICS	ss5634292795	Oct 17, 2022 (156)
50	TOMMO_GENOMICS	ss5697693926	Oct 17, 2022 (156)
51	YY_MCH	ss5804730828	Oct 17, 2022 (156)
52	EVA	ss5843514363	Oct 17, 2022 (156)
53	EVA	ss5854069528	Oct 17, 2022 (156)
54	EVA	ss5862043805	Oct 17, 2022 (156)
55	EVA	ss5962666984	Oct 17, 2022 (156)
56	1000Genomes	NC_000004.11 - 7939578	Oct 12, 2018 (152)
57	1000Genomes_30x	NC_000004.12 - 7937851	Oct 17, 2022 (156)
58	The Avon Longitudinal Study of Parents and Children	NC_000004.11 - 7939578	Oct 12, 2018 (152)
59	Genetic variation in the Estonian population	NC_000004.11 - 7939578	Oct 12, 2018 (152)
60	The Danish reference pan genome	NC_000004.11 - 7939578	Apr 25, 2020 (154)
61	gnomAD - Genomes	NC_000004.12 - 7937851	Apr 26, 2021 (155)
62	Genome of the Netherlands Release 5	NC_000004.11 - 7939578	Apr 25, 2020 (154)
63	KOREAN population from KRGDB	NC_000004.11 - 7939578	Apr 25, 2020 (154)
64	Korean Genome Project	NC_000004.12 - 7937851	Apr 25, 2020 (154)
65	Northern Sweden	NC_000004.11 - 7939578	Jul 13, 2019 (153)
66	Qatari	NC_000004.11 - 7939578	Apr 25, 2020 (154)
67	SGDP_PRJ	NC_000004.11 - 7939578	Apr 25, 2020 (154)
68	Siberian	NC_000004.11 - 7939578	Apr 25, 2020 (154)
69	8.3KJPN	NC_000004.11 - 7939578	Apr 26, 2021 (155)
70	14KJPN	NC_000004.12 - 7937851	Oct 17, 2022 (156)
71	TopMed	NC_000004.12 - 7937851	Apr 26, 2021 (155)
72	UK 10K study - Twins	NC_000004.11 - 7939578	Oct 12, 2018 (152)
73	A Vietnamese Genetic Variation Database	NC_000004.11 - 7939578	Jul 13, 2019 (153)
74	ALFA	NC_000004.12 - 7937851	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
ss111748139, ss163065109, ss198000979, ss277564788, ss1589228372	NC_000004.10:7990477:G:A	NC_000004.12:7937850:G:A	(self)
19665067, 10955598, 7755229, 6568426, 4816966, 11473189, 4114833, 5012838, 10172320, 2685275, 22048464, 10955598, 2394269, ss220729018, ss232249947, ss239573540, ss557294023, ss651050318, ss979733970, ss1071256186, ss1308320055, ss1429763033, ss1580403487, ss1609353042, ss1652347075, ss1800983458, ss1922970908, ss1969651496, ss2022058117, ss2150168921, ss2625530921, ss2705606551, ss2805325005, ss2994091225, ss3345529810, ss3662016981, ss3730829968, ss3761360442, ss3828357458, ss3858155340, ss3904295795, ss5164079157, ss5507380119, ss5634292795, ss5843514363, ss5962666984	NC_000004.11:7939577:G:A	NC_000004.12:7937850:G:A	(self)
25863990, 139482858, 9854528, 31531030, 439368269, 11975084440, ss2260249946, ss3024799027, ss3711352307, ss3804498223, ss3953476527, ss4601990713, ss5257948532, ss5456871566, ss5538338055, ss5697693926, ss5804730828, ss5854069528, ss5862043805	NC_000004.12:7937850:G:A	NC_000004.12:7937850:G:A	(self)
ss6155919, ss105803842, ss156830989	NT_006051.18:6460931:G:A	NC_000004.12:7937850:G:A	(self)
ss10107744	NT_006307.14:53045:G:A	NC_000004.12:7937850:G:A	(self)
11473189, ss3904295795	NC_000004.11:7939577:G:T	NC_000004.12:7937850:G:T	(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 rs4555615

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

rs4555615