Name: rs1001839
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.

rs1001839

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr15:59406649 (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
Variation Type: SNV Single Nucleotide Variation
Frequency: A=0.400325 (105962/264690, TOPMED)
A=0.405749 (56740/139840, GnomAD)
A=0.41068 (11605/28258, 14KJPN) (+ 19 more)
A=0.44555 (12095/27146, ALFA)
A=0.40692 (6820/16760, 8.3KJPN)
A=0.3698 (2368/6404, 1000G_30x)
A=0.3706 (1856/5008, 1000G)
A=0.4817 (2158/4480, Estonian)
A=0.4971 (1916/3854, ALSPAC)
G=0.4668 (1731/3708, TWINSUK)
A=0.4140 (1213/2930, KOREAN)
A=0.3204 (605/1888, HapMap)
A=0.3974 (728/1832, Korea1K)
G=0.445 (444/998, GoNL)
A=0.486 (304/626, Chileans)
G=0.422 (253/600, NorthernSweden)
G=0.348 (126/362, SGDP_PRJ)
A=0.468 (101/216, Qatari)
A=0.458 (97/212, Vietnamese)
G=0.31 (13/42, Siberian)
G=0.50 (20/40, GENOME_DK)
A=0.50 (20/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FAM81A : 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	27146	G=0.55445	A=0.44555
European	Sub	17402	G=0.49615	A=0.50385
African	Sub	4760	G=0.8200	A=0.1800
African Others	Sub	156	G=0.897	A=0.103
African American	Sub	4604	G=0.8173	A=0.1827
Asian	Sub	164	G=0.537	A=0.463
East Asian	Sub	104	G=0.558	A=0.442
Other Asian	Sub	60	G=0.50	A=0.50
Latin American 1	Sub	300	G=0.573	A=0.427
Latin American 2	Sub	2776	G=0.4802	A=0.5198
South Asian	Sub	110	G=0.500	A=0.500
Other	Sub	1634	G=0.5300	A=0.4700

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=0.599675	A=0.400325
gnomAD - Genomes	Global	Study-wide	139840	G=0.594251	A=0.405749
gnomAD - Genomes	European	Sub	75784	G=0.48914	A=0.51086
gnomAD - Genomes	African	Sub	41858	G=0.82023	A=0.17977
gnomAD - Genomes	American	Sub	13606	G=0.48809	A=0.51191
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	G=0.5815	A=0.4185
gnomAD - Genomes	East Asian	Sub	3120	G=0.5926	A=0.4074
gnomAD - Genomes	Other	Sub	2148	G=0.5936	A=0.4064
14KJPN	JAPANESE	Study-wide	28258	G=0.58932	A=0.41068
Allele Frequency Aggregator	Total	Global	27146	G=0.55445	A=0.44555
Allele Frequency Aggregator	European	Sub	17402	G=0.49615	A=0.50385
Allele Frequency Aggregator	African	Sub	4760	G=0.8200	A=0.1800
Allele Frequency Aggregator	Latin American 2	Sub	2776	G=0.4802	A=0.5198
Allele Frequency Aggregator	Other	Sub	1634	G=0.5300	A=0.4700
Allele Frequency Aggregator	Latin American 1	Sub	300	G=0.573	A=0.427
Allele Frequency Aggregator	Asian	Sub	164	G=0.537	A=0.463
Allele Frequency Aggregator	South Asian	Sub	110	G=0.500	A=0.500
8.3KJPN	JAPANESE	Study-wide	16760	G=0.59308	A=0.40692
1000Genomes_30x	Global	Study-wide	6404	G=0.6302	A=0.3698
1000Genomes_30x	African	Sub	1786	G=0.8964	A=0.1036
1000Genomes_30x	Europe	Sub	1266	G=0.5308	A=0.4692
1000Genomes_30x	South Asian	Sub	1202	G=0.5017	A=0.4983
1000Genomes_30x	East Asian	Sub	1170	G=0.5658	A=0.4342
1000Genomes_30x	American	Sub	980	G=0.508	A=0.492
1000Genomes	Global	Study-wide	5008	G=0.6294	A=0.3706
1000Genomes	African	Sub	1322	G=0.8918	A=0.1082
1000Genomes	East Asian	Sub	1008	G=0.5675	A=0.4325
1000Genomes	Europe	Sub	1006	G=0.5358	A=0.4642
1000Genomes	South Asian	Sub	978	G=0.513	A=0.487
1000Genomes	American	Sub	694	G=0.519	A=0.481
Genetic variation in the Estonian population	Estonian	Study-wide	4480	G=0.5183	A=0.4817
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	G=0.5029	A=0.4971
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	G=0.4668	A=0.5332
KOREAN population from KRGDB	KOREAN	Study-wide	2930	G=0.5860	A=0.4140
HapMap	Global	Study-wide	1888	G=0.6796	A=0.3204
HapMap	American	Sub	768	G=0.542	A=0.458
HapMap	African	Sub	690	G=0.896	A=0.104
HapMap	Asian	Sub	254	G=0.579	A=0.421
HapMap	Europe	Sub	176	G=0.580	A=0.420
Korean Genome Project	KOREAN	Study-wide	1832	G=0.6026	A=0.3974
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	G=0.445	A=0.555
Chileans	Chilean	Study-wide	626	G=0.514	A=0.486
Northern Sweden	ACPOP	Study-wide	600	G=0.422	A=0.578
SGDP_PRJ	Global	Study-wide	362	G=0.348	A=0.652
Qatari	Global	Study-wide	216	G=0.532	A=0.468
A Vietnamese Genetic Variation Database	Global	Study-wide	212	G=0.542	A=0.458
Siberian	Global	Study-wide	42	G=0.31	A=0.69
The Danish reference pan genome	Danish	Study-wide	40	G=0.50	A=0.50

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 15	NC_000015.10:g.59406649G>A
GRCh37.p13 chr 15	NC_000015.9:g.59698848G>A

Gene: FAM81A, family with sequence similarity 81 member A (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FAM81A transcript	NM_152450.3:c.	N/A	Genic Upstream Transcript Variant
FAM81A transcript variant X7	XM_011521248.3:c.-22+4291… XM_011521248.3:c.-22+4291G>A	N/A	Intron Variant
FAM81A transcript variant X9	XM_047432170.1:c.-78+4291… XM_047432170.1:c.-78+4291G>A	N/A	Intron Variant
FAM81A transcript variant X12	XM_047432171.1:c.-78+4291… XM_047432171.1:c.-78+4291G>A	N/A	Intron Variant
FAM81A transcript variant X1	XM_005254166.3:c.	N/A	Genic Upstream Transcript Variant
FAM81A transcript variant X8	XM_006720398.4:c.	N/A	Genic Upstream Transcript Variant
FAM81A transcript variant X3	XM_011521247.3:c.	N/A	Genic Upstream Transcript Variant
FAM81A transcript variant X10	XM_011521249.3:c.	N/A	Genic Upstream Transcript Variant
FAM81A transcript variant X11	XM_011521250.3:c.	N/A	Genic Upstream Transcript Variant
FAM81A transcript variant X4	XM_017021931.2:c.	N/A	Genic Upstream Transcript Variant
FAM81A transcript variant X6	XM_017021932.2:c.	N/A	Genic Upstream Transcript Variant
FAM81A transcript variant X13	XM_024449846.2:c.	N/A	Genic Upstream Transcript Variant
FAM81A transcript variant X2	XM_047432168.1:c.	N/A	Genic Upstream Transcript Variant
FAM81A transcript variant X5	XM_047432169.1:c.	N/A	Genic 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
GRCh38.p14 chr 15	NC_000015.10:g.59406649=	NC_000015.10:g.59406649G>A
GRCh37.p13 chr 15	NC_000015.9:g.59698848=	NC_000015.9:g.59698848G>A
FAM81A transcript variant X7	XM_011521248.3:c.-22+4291=	XM_011521248.3:c.-22+4291G>A
FAM81A transcript variant X9	XM_047432170.1:c.-78+4291=	XM_047432170.1:c.-78+4291G>A
FAM81A transcript variant X12	XM_047432171.1:c.-78+4291=	XM_047432171.1:c.-78+4291G>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#.

78 SubSNP, 21 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	TSC-CSHL	ss1462251	Oct 05, 2000 (86)
2	BCM_SSAHASNP	ss10793500	Jul 11, 2003 (116)
3	CSHL-HAPMAP	ss17550359	Feb 27, 2004 (120)
4	SSAHASNP	ss21290363	Apr 05, 2004 (121)
5	ABI	ss43786039	Mar 15, 2006 (126)
6	ILLUMINA	ss65714015	Oct 16, 2006 (127)
7	AFFY	ss66143941	Dec 01, 2006 (127)
8	PERLEGEN	ss69178114	May 17, 2007 (127)
9	AFFY	ss76164781	Dec 07, 2007 (129)
10	KRIBB_YJKIM	ss81449879	Dec 14, 2007 (130)
11	HGSV	ss86098340	Dec 14, 2007 (130)
12	1000GENOMES	ss108862239	Jan 23, 2009 (130)
13	ENSEMBL	ss136887527	Dec 01, 2009 (131)
14	GMI	ss156609092	Dec 01, 2009 (131)
15	COMPLETE_GENOMICS	ss168118089	Jul 04, 2010 (132)
16	ILLUMINA	ss169517070	Jul 04, 2010 (132)
17	COMPLETE_GENOMICS	ss171187986	Jul 04, 2010 (132)
18	AFFY	ss172686521	Jul 04, 2010 (132)
19	BCM-HGSC-SUB	ss207289085	Jul 04, 2010 (132)
20	1000GENOMES	ss211618381	Jul 14, 2010 (132)
21	1000GENOMES	ss226922456	Jul 14, 2010 (132)
22	1000GENOMES	ss236799991	Jul 15, 2010 (132)
23	1000GENOMES	ss243183549	Jul 15, 2010 (132)
24	GMI	ss282279571	May 04, 2012 (137)
25	GMI	ss286963940	Apr 25, 2013 (138)
26	PJP	ss291732005	May 09, 2011 (134)
27	ILLUMINA	ss536565984	Sep 08, 2015 (146)
28	TISHKOFF	ss564515177	Apr 25, 2013 (138)
29	SSMP	ss660246020	Apr 25, 2013 (138)
30	EVA-GONL	ss991845419	Aug 21, 2014 (142)
31	JMKIDD_LAB	ss1080172211	Aug 21, 2014 (142)
32	1000GENOMES	ss1353694262	Aug 21, 2014 (142)
33	DDI	ss1427643802	Apr 01, 2015 (144)
34	EVA_GENOME_DK	ss1577651713	Apr 01, 2015 (144)
35	EVA_UK10K_ALSPAC	ss1633120346	Apr 01, 2015 (144)
36	EVA_UK10K_TWINSUK	ss1676114379	Apr 01, 2015 (144)
37	EVA_DECODE	ss1695865861	Apr 01, 2015 (144)
38	EVA_SVP	ss1713494323	Apr 01, 2015 (144)
39	HAMMER_LAB	ss1808229941	Sep 08, 2015 (146)
40	WEILL_CORNELL_DGM	ss1935251648	Feb 12, 2016 (147)
41	GENOMED	ss1968122737	Jul 19, 2016 (147)
42	JJLAB	ss2028405976	Sep 14, 2016 (149)
43	USC_VALOUEV	ss2156810420	Dec 20, 2016 (150)
44	HUMAN_LONGEVITY	ss2207256511	Dec 20, 2016 (150)
45	SYSTEMSBIOZJU	ss2628698150	Nov 08, 2017 (151)
46	GRF	ss2701283659	Nov 08, 2017 (151)
47	GNOMAD	ss2935557069	Nov 08, 2017 (151)
48	SWEGEN	ss3013375957	Nov 08, 2017 (151)
49	BIOINF_KMB_FNS_UNIBA	ss3028026980	Nov 08, 2017 (151)
50	CSHL	ss3351142272	Nov 08, 2017 (151)
51	ILLUMINA	ss3627374472	Oct 12, 2018 (152)
52	ILLUMINA	ss3638088939	Oct 12, 2018 (152)
53	URBANLAB	ss3650366990	Oct 12, 2018 (152)
54	EGCUT_WGS	ss3680520401	Jul 13, 2019 (153)
55	EVA_DECODE	ss3698004054	Jul 13, 2019 (153)
56	ACPOP	ss3740974146	Jul 13, 2019 (153)
57	EVA	ss3753157623	Jul 13, 2019 (153)
58	KHV_HUMAN_GENOMES	ss3818474442	Jul 13, 2019 (153)
59	EVA	ss3834264467	Apr 27, 2020 (154)
60	EVA	ss3840730870	Apr 27, 2020 (154)
61	EVA	ss3846219862	Apr 27, 2020 (154)
62	SGDP_PRJ	ss3883037156	Apr 27, 2020 (154)
63	KRGDB	ss3932218283	Apr 27, 2020 (154)
64	KOGIC	ss3976254745	Apr 27, 2020 (154)
65	EVA	ss4017704840	Apr 27, 2021 (155)
66	TOPMED	ss4993396920	Apr 27, 2021 (155)
67	TOMMO_GENOMICS	ss5216458613	Apr 27, 2021 (155)
68	1000G_HIGH_COVERAGE	ss5298643022	Oct 16, 2022 (156)
69	EVA	ss5419599549	Oct 16, 2022 (156)
70	HUGCELL_USP	ss5492350486	Oct 16, 2022 (156)
71	1000G_HIGH_COVERAGE	ss5600147234	Oct 16, 2022 (156)
72	SANFORD_IMAGENETICS	ss5657626028	Oct 16, 2022 (156)
73	TOMMO_GENOMICS	ss5770340765	Oct 16, 2022 (156)
74	YY_MCH	ss5815386130	Oct 16, 2022 (156)
75	EVA	ss5828279800	Oct 16, 2022 (156)
76	EVA	ss5851318233	Oct 16, 2022 (156)
77	EVA	ss5876108298	Oct 16, 2022 (156)
78	EVA	ss5949031836	Oct 16, 2022 (156)
79	1000Genomes	NC_000015.9 - 59698848	Oct 12, 2018 (152)
80	1000Genomes_30x	NC_000015.10 - 59406649	Oct 16, 2022 (156)
81	The Avon Longitudinal Study of Parents and Children	NC_000015.9 - 59698848	Oct 12, 2018 (152)
82	Chileans	NC_000015.9 - 59698848	Apr 27, 2020 (154)
83	Genetic variation in the Estonian population	NC_000015.9 - 59698848	Oct 12, 2018 (152)
84	The Danish reference pan genome	NC_000015.9 - 59698848	Apr 27, 2020 (154)
85	gnomAD - Genomes	NC_000015.10 - 59406649	Apr 27, 2021 (155)
86	Genome of the Netherlands Release 5	NC_000015.9 - 59698848	Apr 27, 2020 (154)
87	HapMap	NC_000015.10 - 59406649	Apr 27, 2020 (154)
88	KOREAN population from KRGDB	NC_000015.9 - 59698848	Apr 27, 2020 (154)
89	Korean Genome Project	NC_000015.10 - 59406649	Apr 27, 2020 (154)
90	Northern Sweden	NC_000015.9 - 59698848	Jul 13, 2019 (153)
91	Qatari	NC_000015.9 - 59698848	Apr 27, 2020 (154)
92	SGDP_PRJ	NC_000015.9 - 59698848	Apr 27, 2020 (154)
93	Siberian	NC_000015.9 - 59698848	Apr 27, 2020 (154)
94	8.3KJPN	NC_000015.9 - 59698848	Apr 27, 2021 (155)
95	14KJPN	NC_000015.10 - 59406649	Oct 16, 2022 (156)
96	TopMed	NC_000015.10 - 59406649	Apr 27, 2021 (155)
97	UK 10K study - Twins	NC_000015.9 - 59698848	Oct 12, 2018 (152)
98	A Vietnamese Genetic Variation Database	NC_000015.9 - 59698848	Jul 13, 2019 (153)
99	ALFA	NC_000015.10 - 59406649	Apr 27, 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)
rs56764003	May 23, 2008 (130)
rs57917635	Feb 26, 2009 (130)
rs386508861	Aug 21, 2014 (142)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss86098340, ss108862239, ss168118089, ss171187986, ss207289085, ss211618381, ss282279571, ss286963940, ss291732005, ss1695865861, ss1713494323	NC_000015.8:57486139:G:A	NC_000015.10:59406648:G:A	(self)
66774312, 37070774, 154199, 26258649, 3881118, 16552350, 39395677, 14259011, 17293578, 35054136, 9326774, 74427920, 37070774, 8248947, ss226922456, ss236799991, ss243183549, ss536565984, ss564515177, ss660246020, ss991845419, ss1080172211, ss1353694262, ss1427643802, ss1577651713, ss1633120346, ss1676114379, ss1808229941, ss1935251648, ss1968122737, ss2028405976, ss2156810420, ss2628698150, ss2701283659, ss2935557069, ss3013375957, ss3351142272, ss3627374472, ss3638088939, ss3680520401, ss3740974146, ss3753157623, ss3834264467, ss3840730870, ss3883037156, ss3932218283, ss4017704840, ss5216458613, ss5419599549, ss5657626028, ss5828279800, ss5949031836	NC_000015.9:59698847:G:A	NC_000015.10:59406648:G:A	(self)
87673169, 470739962, 1275565, 32632746, 104177869, 208942580, 2677700397, ss2207256511, ss3028026980, ss3650366990, ss3698004054, ss3818474442, ss3846219862, ss3976254745, ss4993396920, ss5298643022, ss5492350486, ss5600147234, ss5770340765, ss5815386130, ss5851318233, ss5876108298	NC_000015.10:59406648:G:A	NC_000015.10:59406648:G:A	(self)
ss10793500	NT_010194.15:30488458:G:A	NC_000015.10:59406648:G:A	(self)
ss17550359, ss21290363	NT_010194.16:30489404:G:A	NC_000015.10:59406648:G:A	(self)
ss1462251, ss43786039, ss65714015, ss66143941, ss69178114, ss76164781, ss81449879, ss136887527, ss156609092, ss169517070, ss172686521	NT_010194.17:30489404:G:A	NC_000015.10:59406648:G:A	(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 rs1001839

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

rs1001839