Name: rs477777
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.

rs477777

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr3:182873625 (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: T>A / T>C
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.302237 (79999/264690, TOPMED)
T=0.289497 (40551/140074, GnomAD)
C=0.42476 (12003/28258, 14KJPN) (+ 18 more)
T=0.25601 (4836/18890, ALFA)
C=0.42375 (7102/16760, 8.3KJPN)
T=0.3474 (2225/6404, 1000G_30x)
T=0.3536 (1771/5008, 1000G)
T=0.2105 (943/4480, Estonian)
T=0.2299 (886/3854, ALSPAC)
T=0.2228 (826/3708, TWINSUK)
C=0.3928 (1151/2930, KOREAN)
C=0.4099 (751/1832, Korea1K)
T=0.219 (219/998, GoNL)
T=0.247 (148/600, NorthernSweden)
T=0.278 (124/446, SGDP_PRJ)
T=0.394 (85/216, Qatari)
T=0.500 (107/214, Vietnamese)
C=0.500 (107/214, Vietnamese)
C=0.48 (41/86, HapMap)
T=0.13 (7/54, Siberian)
T=0.23 (9/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: ATP11B : 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	T=0.25601	C=0.74399
European	Sub	14286	T=0.23009	C=0.76991
African	Sub	2946	T=0.3381	C=0.6619
African Others	Sub	114	T=0.412	C=0.588
African American	Sub	2832	T=0.3351	C=0.6649
Asian	Sub	112	T=0.482	C=0.518
East Asian	Sub	86	T=0.50	C=0.50
Other Asian	Sub	26	T=0.42	C=0.58
Latin American 1	Sub	146	T=0.342	C=0.658
Latin American 2	Sub	610	T=0.326	C=0.674
South Asian	Sub	98	T=0.29	C=0.71
Other	Sub	692	T=0.321	C=0.679

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	T=0.302237	C=0.697763
gnomAD - Genomes	Global	Study-wide	140074	T=0.289497	C=0.710503
gnomAD - Genomes	European	Sub	75862	T=0.23495	C=0.76505
gnomAD - Genomes	African	Sub	41972	T=0.34678	C=0.65322
gnomAD - Genomes	American	Sub	13640	T=0.33886	C=0.66114
gnomAD - Genomes	Ashkenazi Jewish	Sub	3324	T=0.3541	C=0.6459
gnomAD - Genomes	East Asian	Sub	3126	T=0.5480	C=0.4520
gnomAD - Genomes	Other	Sub	2150	T=0.3070	C=0.6930
14KJPN	JAPANESE	Study-wide	28258	T=0.57524	C=0.42476
Allele Frequency Aggregator	Total	Global	18890	T=0.25601	C=0.74399
Allele Frequency Aggregator	European	Sub	14286	T=0.23009	C=0.76991
Allele Frequency Aggregator	African	Sub	2946	T=0.3381	C=0.6619
Allele Frequency Aggregator	Other	Sub	692	T=0.321	C=0.679
Allele Frequency Aggregator	Latin American 2	Sub	610	T=0.326	C=0.674
Allele Frequency Aggregator	Latin American 1	Sub	146	T=0.342	C=0.658
Allele Frequency Aggregator	Asian	Sub	112	T=0.482	C=0.518
Allele Frequency Aggregator	South Asian	Sub	98	T=0.29	C=0.71
8.3KJPN	JAPANESE	Study-wide	16760	T=0.57625	C=0.42375
1000Genomes_30x	Global	Study-wide	6404	T=0.3474	C=0.6526
1000Genomes_30x	African	Sub	1786	T=0.3639	C=0.6361
1000Genomes_30x	Europe	Sub	1266	T=0.2393	C=0.7607
1000Genomes_30x	South Asian	Sub	1202	T=0.2995	C=0.7005
1000Genomes_30x	East Asian	Sub	1170	T=0.5393	C=0.4607
1000Genomes_30x	American	Sub	980	T=0.287	C=0.713
1000Genomes	Global	Study-wide	5008	T=0.3536	C=0.6464
1000Genomes	African	Sub	1322	T=0.3699	C=0.6301
1000Genomes	East Asian	Sub	1008	T=0.5417	C=0.4583
1000Genomes	Europe	Sub	1006	T=0.2386	C=0.7614
1000Genomes	South Asian	Sub	978	T=0.299	C=0.701
1000Genomes	American	Sub	694	T=0.294	C=0.706
Genetic variation in the Estonian population	Estonian	Study-wide	4480	T=0.2105	C=0.7895
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	T=0.2299	C=0.7701
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	T=0.2228	C=0.7772
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.6072	A=0.0000, C=0.3928
Korean Genome Project	KOREAN	Study-wide	1832	T=0.5901	C=0.4099
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	T=0.219	C=0.781
Northern Sweden	ACPOP	Study-wide	600	T=0.247	C=0.753
SGDP_PRJ	Global	Study-wide	446	T=0.278	C=0.722
Qatari	Global	Study-wide	216	T=0.394	C=0.606
A Vietnamese Genetic Variation Database	Global	Study-wide	214	T=0.500	C=0.500
HapMap	Global	Study-wide	86	T=0.52	C=0.48
HapMap	Asian	Sub	86	T=0.52	C=0.48
Siberian	Global	Study-wide	54	T=0.13	C=0.87
The Danish reference pan genome	Danish	Study-wide	40	T=0.23	C=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 3	NC_000003.12:g.182873625T>A
GRCh38.p14 chr 3	NC_000003.12:g.182873625T>C
GRCh37.p13 chr 3	NC_000003.11:g.182591413T>A
GRCh37.p13 chr 3	NC_000003.11:g.182591413T>C

Gene: ATP11B, ATPase phospholipid transporting 11B (putative) (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
ATP11B transcript	NM_014616.3:c.2049-187T>A	N/A	Intron Variant
ATP11B transcript variant X2	XM_011512593.3:c.2049-187… XM_011512593.3:c.2049-187T>A	N/A	Intron Variant
ATP11B transcript variant X3	XM_011512594.3:c.2049-187… XM_011512594.3:c.2049-187T>A	N/A	Intron Variant
ATP11B transcript variant X4	XM_011512597.3:c.1389-187… XM_011512597.3:c.1389-187T>A	N/A	Intron Variant
ATP11B transcript variant X5	XM_017006008.2:c.1092-187… XM_017006008.2:c.1092-187T>A	N/A	Intron Variant
ATP11B transcript variant X1	XM_047447784.1:c.2049-187… XM_047447784.1:c.2049-187T>A	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	T=	A	C
GRCh38.p14 chr 3	NC_000003.12:g.182873625=	NC_000003.12:g.182873625T>A	NC_000003.12:g.182873625T>C
GRCh37.p13 chr 3	NC_000003.11:g.182591413=	NC_000003.11:g.182591413T>A	NC_000003.11:g.182591413T>C
ATP11B transcript	NM_014616.2:c.2049-187=	NM_014616.2:c.2049-187T>A	NM_014616.2:c.2049-187T>C
ATP11B transcript	NM_014616.3:c.2049-187=	NM_014616.3:c.2049-187T>A	NM_014616.3:c.2049-187T>C
ATP11B transcript variant X1	XM_005247241.1:c.2049-187=	XM_005247241.1:c.2049-187T>A	XM_005247241.1:c.2049-187T>C
ATP11B transcript variant X2	XM_005247242.1:c.2049-187=	XM_005247242.1:c.2049-187T>A	XM_005247242.1:c.2049-187T>C
ATP11B transcript variant X6	XM_005247243.1:c.1503-187=	XM_005247243.1:c.1503-187T>A	XM_005247243.1:c.1503-187T>C
ATP11B transcript variant X4	XM_005247244.1:c.1389-187=	XM_005247244.1:c.1389-187T>A	XM_005247244.1:c.1389-187T>C
ATP11B transcript variant X2	XM_011512593.3:c.2049-187=	XM_011512593.3:c.2049-187T>A	XM_011512593.3:c.2049-187T>C
ATP11B transcript variant X3	XM_011512594.3:c.2049-187=	XM_011512594.3:c.2049-187T>A	XM_011512594.3:c.2049-187T>C
ATP11B transcript variant X4	XM_011512597.3:c.1389-187=	XM_011512597.3:c.1389-187T>A	XM_011512597.3:c.1389-187T>C
ATP11B transcript variant X5	XM_017006008.2:c.1092-187=	XM_017006008.2:c.1092-187T>A	XM_017006008.2:c.1092-187T>C
ATP11B transcript variant X1	XM_047447784.1:c.2049-187=	XM_047447784.1:c.2049-187T>A	XM_047447784.1:c.2049-187T>C

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#.

77 SubSNP, 20 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	SC_JCM	ss647264	Aug 11, 2000 (83)
2	TSC-CSHL	ss2959473	Apr 12, 2001 (94)
3	BCM_SSAHASNP	ss14165426	Dec 05, 2003 (119)
4	SSAHASNP	ss21877529	Apr 05, 2004 (121)
5	PERLEGEN	ss23973494	Sep 20, 2004 (123)
6	BCMHGSC_JDW	ss92394715	Mar 24, 2008 (129)
7	HUMANGENOME_JCVI	ss99154194	Feb 03, 2009 (130)
8	1000GENOMES	ss111466991	Jan 25, 2009 (130)
9	1000GENOMES	ss112745543	Jan 25, 2009 (130)
10	ILLUMINA-UK	ss117407549	Feb 14, 2009 (130)
11	ENSEMBL	ss135409799	Dec 01, 2009 (131)
12	ENSEMBL	ss139328453	Dec 01, 2009 (131)
13	GMI	ss156578815	Dec 01, 2009 (131)
14	COMPLETE_GENOMICS	ss162885856	Jul 04, 2010 (132)
15	COMPLETE_GENOMICS	ss165168155	Jul 04, 2010 (132)
16	COMPLETE_GENOMICS	ss167482204	Jul 04, 2010 (132)
17	BUSHMAN	ss203616887	Jul 04, 2010 (132)
18	BCM-HGSC-SUB	ss206074126	Jul 04, 2010 (132)
19	1000GENOMES	ss220621800	Jul 14, 2010 (132)
20	1000GENOMES	ss232172688	Jul 14, 2010 (132)
21	1000GENOMES	ss239512227	Jul 15, 2010 (132)
22	BL	ss253727326	May 09, 2011 (134)
23	GMI	ss277483844	May 04, 2012 (137)
24	PJP	ss292987709	May 09, 2011 (134)
25	TISHKOFF	ss557166078	Apr 25, 2013 (138)
26	SSMP	ss650911719	Apr 25, 2013 (138)
27	EVA-GONL	ss979536489	Aug 21, 2014 (142)
28	JMKIDD_LAB	ss1071115413	Aug 21, 2014 (142)
29	1000GENOMES	ss1307579908	Aug 21, 2014 (142)
30	DDI	ss1429695368	Apr 01, 2015 (144)
31	EVA_GENOME_DK	ss1580326502	Apr 01, 2015 (144)
32	EVA_DECODE	ss1589033675	Apr 01, 2015 (144)
33	EVA_UK10K_ALSPAC	ss1608968431	Apr 01, 2015 (144)
34	EVA_UK10K_TWINSUK	ss1651962464	Apr 01, 2015 (144)
35	HAMMER_LAB	ss1800555556	Sep 08, 2015 (146)
36	WEILL_CORNELL_DGM	ss1922755974	Feb 12, 2016 (147)
37	GENOMED	ss1969607293	Jul 19, 2016 (147)
38	JJLAB	ss2021953990	Sep 14, 2016 (149)
39	USC_VALOUEV	ss2150051658	Dec 20, 2016 (150)
40	HUMAN_LONGEVITY	ss2258812464	Dec 20, 2016 (150)
41	SYSTEMSBIOZJU	ss2625475482	Nov 08, 2017 (151)
42	GRF	ss2705474587	Nov 08, 2017 (151)
43	GNOMAD	ss2803220380	Nov 08, 2017 (151)
44	SWEGEN	ss2993764587	Nov 08, 2017 (151)
45	BIOINF_KMB_FNS_UNIBA	ss3024745091	Nov 08, 2017 (151)
46	CSHL	ss3345428296	Nov 08, 2017 (151)
47	URBANLAB	ss3647601201	Oct 12, 2018 (152)
48	EGCUT_WGS	ss3661722950	Jul 13, 2019 (153)
49	EVA_DECODE	ss3710975673	Jul 13, 2019 (153)
50	ACPOP	ss3730659308	Jul 13, 2019 (153)
51	EVA	ss3761126444	Jul 13, 2019 (153)
52	PACBIO	ss3784556330	Jul 13, 2019 (153)
53	PACBIO	ss3790034640	Jul 13, 2019 (153)
54	PACBIO	ss3794909341	Jul 13, 2019 (153)
55	KHV_HUMAN_GENOMES	ss3804263533	Jul 13, 2019 (153)
56	EVA	ss3828255888	Apr 25, 2020 (154)
57	EVA	ss3837559921	Apr 25, 2020 (154)
58	EVA	ss3842992391	Apr 25, 2020 (154)
59	SGDP_PRJ	ss3857721948	Apr 25, 2020 (154)
60	KRGDB	ss3903805437	Apr 25, 2020 (154)
61	KOGIC	ss3953088516	Apr 25, 2020 (154)
62	TOPMED	ss4596084503	Apr 26, 2021 (155)
63	TOMMO_GENOMICS	ss5163191377	Apr 26, 2021 (155)
64	1000G_HIGH_COVERAGE	ss5257270633	Oct 13, 2022 (156)
65	EVA	ss5345546285	Oct 13, 2022 (156)
66	HUGCELL_USP	ss5456291033	Oct 13, 2022 (156)
67	EVA	ss5507333674	Oct 13, 2022 (156)
68	1000G_HIGH_COVERAGE	ss5537370441	Oct 13, 2022 (156)
69	SANFORD_IMAGENETICS	ss5633902022	Oct 13, 2022 (156)
70	TOMMO_GENOMICS	ss5696529761	Oct 13, 2022 (156)
71	EVA	ss5800111385	Oct 13, 2022 (156)
72	YY_MCH	ss5804553110	Oct 13, 2022 (156)
73	EVA	ss5826959946	Oct 13, 2022 (156)
74	EVA	ss5853989056	Oct 13, 2022 (156)
75	EVA	ss5872430671	Oct 13, 2022 (156)
76	EVA	ss5962283934	Oct 13, 2022 (156)
77	EVA	ss5980190168	Oct 13, 2022 (156)
78	1000Genomes	NC_000003.11 - 182591413	Oct 12, 2018 (152)
79	1000Genomes_30x	NC_000003.12 - 182873625	Oct 13, 2022 (156)
80	The Avon Longitudinal Study of Parents and Children	NC_000003.11 - 182591413	Oct 12, 2018 (152)
81	Genetic variation in the Estonian population	NC_000003.11 - 182591413	Oct 12, 2018 (152)
82	The Danish reference pan genome	NC_000003.11 - 182591413	Apr 25, 2020 (154)
83	gnomAD - Genomes	NC_000003.12 - 182873625	Apr 26, 2021 (155)
84	Genome of the Netherlands Release 5	NC_000003.11 - 182591413	Apr 25, 2020 (154)
85	HapMap	NC_000003.12 - 182873625	Apr 25, 2020 (154)
86	KOREAN population from KRGDB	NC_000003.11 - 182591413	Apr 25, 2020 (154)
87	Korean Genome Project	NC_000003.12 - 182873625	Apr 25, 2020 (154)
88	Northern Sweden	NC_000003.11 - 182591413	Jul 13, 2019 (153)
89	Qatari	NC_000003.11 - 182591413	Apr 25, 2020 (154)
90	SGDP_PRJ	NC_000003.11 - 182591413	Apr 25, 2020 (154)
91	Siberian	NC_000003.11 - 182591413	Apr 25, 2020 (154)
92	8.3KJPN	NC_000003.11 - 182591413	Apr 26, 2021 (155)
93	14KJPN	NC_000003.12 - 182873625	Oct 13, 2022 (156)
94	TopMed	NC_000003.12 - 182873625	Apr 26, 2021 (155)
95	UK 10K study - Twins	NC_000003.11 - 182591413	Oct 12, 2018 (152)
96	A Vietnamese Genetic Variation Database	NC_000003.11 - 182591413	Jul 13, 2019 (153)
97	ALFA	NC_000003.12 - 182873625	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
10982831, ss3903805437	NC_000003.11:182591412:T:A	NC_000003.12:182873624:T:A	(self)
ss92394715, ss111466991, ss112745543, ss117407549, ss162885856, ss165168155, ss167482204, ss203616887, ss206074126, ss253727326, ss277483844, ss292987709, ss1589033675	NC_000003.10:184074106:T:C	NC_000003.12:182873624:T:C	(self)
18898277, 10532346, 7461198, 6491441, 4628819, 10982831, 3944173, 4797904, 9738928, 2568012, 21160684, 10532346, 2302796, ss220621800, ss232172688, ss239512227, ss557166078, ss650911719, ss979536489, ss1071115413, ss1307579908, ss1429695368, ss1580326502, ss1608968431, ss1651962464, ss1800555556, ss1922755974, ss1969607293, ss2021953990, ss2150051658, ss2625475482, ss2705474587, ss2803220380, ss2993764587, ss3345428296, ss3661722950, ss3730659308, ss3761126444, ss3784556330, ss3790034640, ss3794909341, ss3828255888, ss3837559921, ss3857721948, ss3903805437, ss5163191377, ss5345546285, ss5507333674, ss5633902022, ss5800111385, ss5826959946, ss5962283934, ss5980190168	NC_000003.11:182591412:T:C	NC_000003.12:182873624:T:C	(self)
24896376, 134256301, 2523185, 9466517, 30366865, 433462058, 2039197037, ss2258812464, ss3024745091, ss3647601201, ss3710975673, ss3804263533, ss3842992391, ss3953088516, ss4596084503, ss5257270633, ss5456291033, ss5537370441, ss5696529761, ss5804553110, ss5853989056, ss5872430671	NC_000003.12:182873624:T:C	NC_000003.12:182873624:T:C	(self)
ss14165426, ss21877529	NT_005612.14:89086570:T:C	NC_000003.12:182873624:T:C	(self)
ss647264, ss2959473, ss23973494, ss99154194, ss135409799, ss139328453, ss156578815	NT_005612.16:89086558:T:C	NC_000003.12:182873624:T: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 rs477777

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

rs477777