Name: rs2980439
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.

rs2980439

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr8:8237348 (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 / G>T
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.472428 (125047/264690, TOPMED)
A=0.462489 (64778/140064, GnomAD)
G=0.17246 (4873/28256, 14KJPN) (+ 16 more)
A=0.44595 (8424/18890, ALFA)
G=0.17037 (2855/16758, 8.3KJPN)
G=0.4744 (3038/6404, 1000G_30x)
G=0.4639 (2323/5008, 1000G)
A=0.4798 (1849/3854, ALSPAC)
A=0.4763 (1766/3708, TWINSUK)
G=0.2003 (587/2930, KOREAN)
G=0.1867 (342/1832, Korea1K)
A=0.477 (476/998, GoNL)
G=0.495 (297/600, NorthernSweden)
A=0.391 (209/534, MGP)
G=0.218 (97/444, SGDP_PRJ)
A=0.490 (150/306, HapMap)
A=0.412 (89/216, Qatari)
G=0.279 (58/208, Vietnamese)
G=0.22 (10/46, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FAM86B3P : Intron 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: 20230706150541

Population	Group	Sample Size	Ref Allele	Alt Allele
Total	Global	18890	G=0.55405	A=0.44595
European	Sub	14286	G=0.54522	A=0.45478
African	Sub	2946	G=0.6768	A=0.3232
African Others	Sub	114	G=0.658	A=0.342
African American	Sub	2832	G=0.6776	A=0.3224
Asian	Sub	112	G=0.196	A=0.804
East Asian	Sub	86	G=0.19	A=0.81
Other Asian	Sub	26	G=0.23	A=0.77
Latin American 1	Sub	146	G=0.479	A=0.521
Latin American 2	Sub	610	G=0.310	A=0.690
South Asian	Sub	98	G=0.44	A=0.56
Other	Sub	692	G=0.519	A=0.481

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=0.527572	A=0.472428
gnomAD - Genomes	Global	Study-wide	140064	G=0.537511	A=0.462489
gnomAD - Genomes	European	Sub	75846	G=0.50498	A=0.49502
gnomAD - Genomes	African	Sub	41988	G=0.66679	A=0.33321
gnomAD - Genomes	American	Sub	13636	G=0.38010	A=0.61990
gnomAD - Genomes	Ashkenazi Jewish	Sub	3320	G=0.6301	A=0.3699
gnomAD - Genomes	East Asian	Sub	3126	G=0.2012	A=0.7988
gnomAD - Genomes	Other	Sub	2148	G=0.5047	A=0.4953
14KJPN	JAPANESE	Study-wide	28256	G=0.17246	A=0.82754
Allele Frequency Aggregator	Total	Global	18890	G=0.55405	A=0.44595
Allele Frequency Aggregator	European	Sub	14286	G=0.54522	A=0.45478
Allele Frequency Aggregator	African	Sub	2946	G=0.6768	A=0.3232
Allele Frequency Aggregator	Other	Sub	692	G=0.519	A=0.481
Allele Frequency Aggregator	Latin American 2	Sub	610	G=0.310	A=0.690
Allele Frequency Aggregator	Latin American 1	Sub	146	G=0.479	A=0.521
Allele Frequency Aggregator	Asian	Sub	112	G=0.196	A=0.804
Allele Frequency Aggregator	South Asian	Sub	98	G=0.44	A=0.56
8.3KJPN	JAPANESE	Study-wide	16758	G=0.17037	A=0.82963
1000Genomes_30x	Global	Study-wide	6404	G=0.4744	A=0.5256
1000Genomes_30x	African	Sub	1786	G=0.6892	A=0.3108
1000Genomes_30x	Europe	Sub	1266	G=0.5569	A=0.4431
1000Genomes_30x	South Asian	Sub	1202	G=0.4401	A=0.5599
1000Genomes_30x	East Asian	Sub	1170	G=0.1880	A=0.8120
1000Genomes_30x	American	Sub	980	G=0.360	A=0.640
1000Genomes	Global	Study-wide	5008	G=0.4639	A=0.5361
1000Genomes	African	Sub	1322	G=0.6876	A=0.3124
1000Genomes	East Asian	Sub	1008	G=0.1786	A=0.8214
1000Genomes	Europe	Sub	1006	G=0.5457	A=0.4543
1000Genomes	South Asian	Sub	978	G=0.441	A=0.559
1000Genomes	American	Sub	694	G=0.366	A=0.634
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.5202	A=0.4798
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.5237	A=0.4763
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.2003	A=0.7997, C=0.0000, T=0.0000
Korean Genome Project	KOREAN	Study-wide	1832	G=0.1867	A=0.8133
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.523	A=0.477
Northern Sweden	ACPOP	Study-wide	600	G=0.495	A=0.505
Medical Genome Project healthy controls from Spanish population	Spanish controls	Study-wide	534	G=0.609	A=0.391
SGDP_PRJ	Global	Study-wide	444	G=0.218	A=0.782
HapMap	Global	Study-wide	306	G=0.510	A=0.490
HapMap	African	Sub	110	G=0.745	A=0.255
HapMap	American	Sub	110	G=0.564	A=0.436
HapMap	Asian	Sub	86	G=0.14	A=0.86
Qatari	Global	Study-wide	216	G=0.588	A=0.412
A Vietnamese Genetic Variation Database	Global	Study-wide	208	G=0.279	A=0.721
Siberian	Global	Study-wide	46	G=0.22	A=0.78

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 8	NC_000008.11:g.8237348G>A
GRCh38.p14 chr 8	NC_000008.11:g.8237348G>C
GRCh38.p14 chr 8	NC_000008.11:g.8237348G>T
GRCh37.p13 chr 8	NC_000008.10:g.8094870G>A
GRCh37.p13 chr 8	NC_000008.10:g.8094870G>C
GRCh37.p13 chr 8	NC_000008.10:g.8094870G>T
ALG1L13P pseudogene	NG_044407.1:g.7420C>T
ALG1L13P pseudogene	NG_044407.1:g.7420C>G
ALG1L13P pseudogene	NG_044407.1:g.7420C>A
GRCh38.p14 chr 8 fix patch HG76_PATCH	NW_018654717.1:g.5110517C>T
GRCh38.p14 chr 8 fix patch HG76_PATCH	NW_018654717.1:g.5110517C>G
GRCh38.p14 chr 8 fix patch HG76_PATCH	NW_018654717.1:g.5110517C>A

Gene: FAM86B3P, family with sequence similarity 86 member B3, pseudogene (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FAM86B3P transcript variant 2	NR_024361.1:n.	N/A	Intron Variant
FAM86B3P transcript variant 1	NR_024362.1:n.	N/A	Intron Variant
FAM86B3P transcript variant 3	NR_024363.1:n.	N/A	Intron 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	T
GRCh38.p14 chr 8	NC_000008.11:g.8237348=	NC_000008.11:g.8237348G>A	NC_000008.11:g.8237348G>C	NC_000008.11:g.8237348G>T
GRCh37.p13 chr 8	NC_000008.10:g.8094870=	NC_000008.10:g.8094870G>A	NC_000008.10:g.8094870G>C	NC_000008.10:g.8094870G>T
ALG1L13P pseudogene	NG_044407.1:g.7420=	NG_044407.1:g.7420C>T	NG_044407.1:g.7420C>G	NG_044407.1:g.7420C>A
GRCh38.p14 chr 8 fix patch HG76_PATCH	NW_018654717.1:g.5110517=	NW_018654717.1:g.5110517C>T	NW_018654717.1:g.5110517C>G	NW_018654717.1:g.5110517C>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#.

74 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss4194676	Nov 05, 2001 (101)
2	WI_SSAHASNP	ss11916026	Jul 11, 2003 (116)
3	CSHL-HAPMAP	ss17212188	Feb 27, 2004 (120)
4	SSAHASNP	ss22686706	Apr 05, 2004 (121)
5	ABI	ss43253082	Mar 14, 2006 (126)
6	HGSV	ss77204244	Dec 07, 2007 (129)
7	HGSV	ss82041316	Dec 15, 2007 (130)
8	BCMHGSC_JDW	ss93827194	Mar 25, 2008 (129)
9	HUMANGENOME_JCVI	ss98045136	Feb 06, 2009 (130)
10	1000GENOMES	ss112785342	Jan 25, 2009 (130)
11	ENSEMBL	ss133520534	Dec 01, 2009 (131)
12	ENSEMBL	ss143230507	Dec 01, 2009 (131)
13	GMI	ss155958495	Dec 01, 2009 (131)
14	BUSHMAN	ss198725449	Jul 04, 2010 (132)
15	1000GENOMES	ss223514260	Jul 14, 2010 (132)
16	1000GENOMES	ss234299599	Jul 15, 2010 (132)
17	1000GENOMES	ss241186731	Jul 15, 2010 (132)
18	BL	ss254061747	May 09, 2011 (134)
19	GMI	ss279671598	May 04, 2012 (137)
20	GMI	ss285781984	Apr 25, 2013 (138)
21	PJP	ss294138389	May 09, 2011 (134)
22	ILLUMINA	ss410927671	Sep 17, 2011 (135)
23	TISHKOFF	ss560515600	Apr 25, 2013 (138)
24	SSMP	ss654946142	Apr 25, 2013 (138)
25	EVA-GONL	ss985142419	Aug 21, 2014 (142)
26	JMKIDD_LAB	ss1075235675	Aug 21, 2014 (142)
27	1000GENOMES	ss1328423513	Aug 21, 2014 (142)
28	DDI	ss1431397178	Apr 01, 2015 (144)
29	EVA_DECODE	ss1594728570	Apr 01, 2015 (144)
30	EVA_UK10K_ALSPAC	ss1619875025	Apr 01, 2015 (144)
31	EVA_UK10K_TWINSUK	ss1662869058	Apr 01, 2015 (144)
32	EVA_MGP	ss1711191226	Apr 01, 2015 (144)
33	HAMMER_LAB	ss1805376053	Sep 08, 2015 (146)
34	WEILL_CORNELL_DGM	ss1928426341	Feb 12, 2016 (147)
35	GENOMED	ss1970896216	Jul 19, 2016 (147)
36	JJLAB	ss2024904747	Sep 14, 2016 (149)
37	USC_VALOUEV	ss2153130243	Dec 20, 2016 (150)
38	SYSTEMSBIOZJU	ss2626939722	Nov 08, 2017 (151)
39	GRF	ss2708883108	Nov 08, 2017 (151)
40	GNOMAD	ss2862747149	Nov 08, 2017 (151)
41	SWEGEN	ss3002597278	Nov 08, 2017 (151)
42	BIOINF_KMB_FNS_UNIBA	ss3026241668	Nov 08, 2017 (151)
43	CSHL	ss3348017681	Nov 08, 2017 (151)
44	OMUKHERJEE_ADBS	ss3646370805	Oct 12, 2018 (152)
45	URBANLAB	ss3648836807	Oct 12, 2018 (152)
46	EVA_DECODE	ss3721322751	Jul 13, 2019 (153)
47	ACPOP	ss3735357974	Jul 13, 2019 (153)
48	EVA	ss3767563276	Jul 13, 2019 (153)
49	PACBIO	ss3786050419	Jul 13, 2019 (153)
50	PACBIO	ss3791320285	Jul 13, 2019 (153)
51	PACBIO	ss3796201330	Jul 13, 2019 (153)
52	KHV_HUMAN_GENOMES	ss3810725781	Jul 13, 2019 (153)
53	EVA	ss3830988090	Apr 26, 2020 (154)
54	EVA	ss3838999504	Apr 26, 2020 (154)
55	EVA	ss3844458506	Apr 26, 2020 (154)
56	SGDP_PRJ	ss3869163376	Apr 26, 2020 (154)
57	KRGDB	ss3916578814	Apr 26, 2020 (154)
58	KOGIC	ss3963172641	Apr 26, 2020 (154)
59	FSA-LAB	ss3984390943	Apr 26, 2021 (155)
60	FSA-LAB	ss3984390944	Apr 26, 2021 (155)
61	TOPMED	ss4774159003	Apr 26, 2021 (155)
62	TOMMO_GENOMICS	ss5187107093	Apr 26, 2021 (155)
63	1000G_HIGH_COVERAGE	ss5275904618	Oct 13, 2022 (156)
64	EVA	ss5378869712	Oct 13, 2022 (156)
65	HUGCELL_USP	ss5472604690	Oct 13, 2022 (156)
66	1000G_HIGH_COVERAGE	ss5565608262	Oct 13, 2022 (156)
67	SANFORD_IMAGENETICS	ss5644670698	Oct 13, 2022 (156)
68	TOMMO_GENOMICS	ss5728573927	Oct 13, 2022 (156)
69	YY_MCH	ss5809402943	Oct 13, 2022 (156)
70	EVA	ss5830056101	Oct 13, 2022 (156)
71	EVA	ss5856232997	Oct 13, 2022 (156)
72	EVA	ss5887542222	Oct 13, 2022 (156)
73	EVA	ss5973851097	Oct 13, 2022 (156)
74	EVA	ss5981247745	Oct 13, 2022 (156)
75	1000Genomes	NC_000008.10 - 8094870	Oct 12, 2018 (152)
76	1000Genomes_30x	NC_000008.11 - 8237348	Oct 13, 2022 (156)
77	The Avon Longitudinal Study of Parents and Children	NC_000008.10 - 8094870	Oct 12, 2018 (152)
78	gnomAD - Genomes	NC_000008.11 - 8237348	Apr 26, 2021 (155)
79	Genome of the Netherlands Release 5	NC_000008.10 - 8094870	Apr 26, 2020 (154)
80	HapMap	NC_000008.11 - 8237348	Apr 26, 2020 (154)
81	KOREAN population from KRGDB	NC_000008.10 - 8094870	Apr 26, 2020 (154)
82	Korean Genome Project	NC_000008.11 - 8237348	Apr 26, 2020 (154)
83	Medical Genome Project healthy controls from Spanish population	NC_000008.10 - 8094870	Apr 26, 2020 (154)
84	Northern Sweden	NC_000008.10 - 8094870	Jul 13, 2019 (153)
85	Qatari	NC_000008.10 - 8094870	Apr 26, 2020 (154)
86	SGDP_PRJ	NC_000008.10 - 8094870	Apr 26, 2020 (154)
87	Siberian	NC_000008.10 - 8094870	Apr 26, 2020 (154)
88	8.3KJPN	NC_000008.10 - 8094870	Apr 26, 2021 (155)
89	14KJPN	NC_000008.11 - 8237348	Oct 13, 2022 (156)
90	TopMed	NC_000008.11 - 8237348	Apr 26, 2021 (155)
91	UK 10K study - Twins	NC_000008.10 - 8094870	Oct 12, 2018 (152)
92	A Vietnamese Genetic Variation Database	NC_000008.10 - 8094870	Jul 13, 2019 (153)
93	ALFA	NC_000008.11 - 8237348	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).

Associated ID	History Updated (Build)
rs61044392	May 26, 2008 (130)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77204244, ss82041316, ss93827194, ss112785342, ss198725449, ss254061747, ss279671598, ss285781984, ss294138389, ss1594728570	NC_000008.9:8132279:G:A	NC_000008.11:8237347:G:A	(self)
40506616, 22519276, 10059828, 23756208, 306986, 8642839, 10468271, 21180356, 5646597, 45076400, 22519276, 5016944, ss223514260, ss234299599, ss241186731, ss560515600, ss654946142, ss985142419, ss1075235675, ss1328423513, ss1431397178, ss1619875025, ss1662869058, ss1711191226, ss1805376053, ss1928426341, ss1970896216, ss2024904747, ss2153130243, ss2626939722, ss2708883108, ss2862747149, ss3002597278, ss3348017681, ss3646370805, ss3735357974, ss3767563276, ss3786050419, ss3791320285, ss3796201330, ss3830988090, ss3838999504, ss3869163376, ss3916578814, ss3984390943, ss3984390944, ss5187107093, ss5378869712, ss5644670698, ss5830056101, ss5973851097, ss5981247745	NC_000008.10:8094869:G:A	NC_000008.11:8237347:G:A	(self)
53134197, 285771860, 3555242, 19550642, 62411031, 611536563, 9924021779, ss3026241668, ss3648836807, ss3721322751, ss3810725781, ss3844458506, ss3963172641, ss4774159003, ss5275904618, ss5472604690, ss5565608262, ss5728573927, ss5809402943, ss5856232997, ss5887542222	NC_000008.11:8237347:G:A	NC_000008.11:8237347:G:A	(self)
ss11916026	NT_077531.2:404902:G:A	NC_000008.11:8237347:G:A	(self)
ss17212188, ss22686706	NT_077531.3:570220:G:A	NC_000008.11:8237347:G:A	(self)
ss4194676, ss43253082, ss98045136, ss133520534, ss143230507, ss155958495, ss410927671	NT_077531.4:570220:G:A	NC_000008.11:8237347:G:A	(self)
23756208, ss3916578814	NC_000008.10:8094869:G:C	NC_000008.11:8237347:G:C	(self)
23756208, ss3916578814	NC_000008.10:8094869:G:T	NC_000008.11:8237347: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 rs2980439

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.

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dbSNP Short Genetic Variations

Welcome to the Reference SNP (rs) Report

Reference SNP (rs) Report

rs2980439