Name: rs4646919
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.

rs4646919

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:34886114 (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: C>A / C>G / C>T
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.078711 (20834/264690, TOPMED)
T=0.26226 (7411/28258, 14KJPN)
T=0.01136 (199/17510, ALFA) (+ 14 more)
T=0.26104 (4375/16760, 8.3KJPN)
T=0.1369 (877/6404, 1000G_30x)
T=0.1382 (692/5008, 1000G)
T=0.0290 (130/4480, Estonian)
T=0.0278 (107/3854, ALSPAC)
T=0.0267 (99/3708, TWINSUK)
T=0.2304 (675/2930, KOREAN)
T=0.021 (21/998, GoNL)
T=0.037 (22/600, NorthernSweden)
T=0.074 (16/216, Qatari)
C=0.439 (50/114, SGDP_PRJ)
T=0.05 (2/40, GENOME_DK)
C=0.5 (4/8, Siberian)
T=0.5 (4/8, Siberian)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TAF11 : 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	17510	C=0.98864	A=0.00000, G=0.00000, T=0.01136
European	Sub	13844	C=0.98707	A=0.00000, G=0.00000, T=0.01293
African	Sub	2260	C=0.9956	A=0.0000, G=0.0000, T=0.0044
African Others	Sub	82	C=1.00	A=0.00, G=0.00, T=0.00
African American	Sub	2178	C=0.9954	A=0.0000, G=0.0000, T=0.0046
Asian	Sub	80	C=0.99	A=0.00, G=0.00, T=0.01
East Asian	Sub	58	C=0.98	A=0.00, G=0.00, T=0.02
Other Asian	Sub	22	C=1.00	A=0.00, G=0.00, T=0.00
Latin American 1	Sub	116	C=1.000	A=0.000, G=0.000, T=0.000
Latin American 2	Sub	532	C=1.000	A=0.000, G=0.000, T=0.000
South Asian	Sub	74	C=1.00	A=0.00, G=0.00, T=0.00
Other	Sub	604	C=0.985	A=0.000, G=0.000, T=0.015

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	C=0.921289	T=0.078711
14KJPN	JAPANESE	Study-wide	28258	C=0.73774	T=0.26226
Allele Frequency Aggregator	Total	Global	17510	C=0.98864	A=0.00000, G=0.00000, T=0.01136
Allele Frequency Aggregator	European	Sub	13844	C=0.98707	A=0.00000, G=0.00000, T=0.01293
Allele Frequency Aggregator	African	Sub	2260	C=0.9956	A=0.0000, G=0.0000, T=0.0044
Allele Frequency Aggregator	Other	Sub	604	C=0.985	A=0.000, G=0.000, T=0.015
Allele Frequency Aggregator	Latin American 2	Sub	532	C=1.000	A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator	Latin American 1	Sub	116	C=1.000	A=0.000, G=0.000, T=0.000
Allele Frequency Aggregator	Asian	Sub	80	C=0.99	A=0.00, G=0.00, T=0.01
Allele Frequency Aggregator	South Asian	Sub	74	C=1.00	A=0.00, G=0.00, T=0.00
8.3KJPN	JAPANESE	Study-wide	16760	C=0.73896	T=0.26104
1000Genomes_30x	Global	Study-wide	6404	C=0.8631	T=0.1369
1000Genomes_30x	African	Sub	1786	C=0.8488	T=0.1512
1000Genomes_30x	Europe	Sub	1266	C=0.9621	T=0.0379
1000Genomes_30x	South Asian	Sub	1202	C=0.8636	T=0.1364
1000Genomes_30x	East Asian	Sub	1170	C=0.7410	T=0.2590
1000Genomes_30x	American	Sub	980	C=0.906	T=0.094
1000Genomes	Global	Study-wide	5008	C=0.8618	T=0.1382
1000Genomes	African	Sub	1322	C=0.8533	T=0.1467
1000Genomes	East Asian	Sub	1008	C=0.7411	T=0.2589
1000Genomes	Europe	Sub	1006	C=0.9622	T=0.0378
1000Genomes	South Asian	Sub	978	C=0.864	T=0.136
1000Genomes	American	Sub	694	C=0.905	T=0.095
Genetic variation in the Estonian population	Estonian	Study-wide	4480	C=0.9710	T=0.0290
The Avon Longitudinal Study of Parents and Children	PARENT AND CHILD COHORT	Study-wide	3854	C=0.9722	T=0.0278
UK 10K study - Twins	TWIN COHORT	Study-wide	3708	C=0.9733	T=0.0267
KOREAN population from KRGDB	KOREAN	Study-wide	2930	C=0.7696	T=0.2304
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	C=0.979	T=0.021
Northern Sweden	ACPOP	Study-wide	600	C=0.963	T=0.037
Qatari	Global	Study-wide	216	C=0.926	T=0.074
SGDP_PRJ	Global	Study-wide	114	C=0.439	T=0.561
The Danish reference pan genome	Danish	Study-wide	40	C=0.95	T=0.05
Siberian	Global	Study-wide	8	C=0.5	T=0.5

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 6	NC_000006.12:g.34886114C>A
GRCh38.p14 chr 6	NC_000006.12:g.34886114C>G
GRCh38.p14 chr 6	NC_000006.12:g.34886114C>T
GRCh37.p13 chr 6	NC_000006.11:g.34853891C>A
GRCh37.p13 chr 6	NC_000006.11:g.34853891C>G
GRCh37.p13 chr 6	NC_000006.11:g.34853891C>T

Gene: TAF11, TATA-box binding protein associated factor 11 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TAF11 transcript variant 2	NM_001270488.1:c.171+1673… NM_001270488.1:c.171+1673G>T	N/A	Intron Variant
TAF11 transcript variant 1	NM_005643.4:c.171+1673G>T	N/A	Intron Variant
TAF11 transcript variant X1	XM_011514827.3:c.	N/A	Genic Upstream Transcript Variant
TAF11 transcript variant X2	XM_047419270.1: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	C=	A	G	T
GRCh38.p14 chr 6	NC_000006.12:g.34886114=	NC_000006.12:g.34886114C>A	NC_000006.12:g.34886114C>G	NC_000006.12:g.34886114C>T
GRCh37.p13 chr 6	NC_000006.11:g.34853891=	NC_000006.11:g.34853891C>A	NC_000006.11:g.34853891C>G	NC_000006.11:g.34853891C>T
TAF11 transcript variant 2	NM_001270488.1:c.171+1673=	NM_001270488.1:c.171+1673G>T	NM_001270488.1:c.171+1673G>C	NM_001270488.1:c.171+1673G>A
TAF11 transcript variant 1	NM_005643.3:c.171+1673=	NM_005643.3:c.171+1673G>T	NM_005643.3:c.171+1673G>C	NM_005643.3:c.171+1673G>A
TAF11 transcript variant 1	NM_005643.4:c.171+1673=	NM_005643.4:c.171+1673G>T	NM_005643.4:c.171+1673G>C	NM_005643.4:c.171+1673G>A
TAF11 transcript variant X1	XM_005249330.1:c.345+1673=	XM_005249330.1:c.345+1673G>T	XM_005249330.1:c.345+1673G>C	XM_005249330.1:c.345+1673G>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#.

50 SubSNP, 19 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	EGP_SNPS	ss6312483	Feb 20, 2003 (111)
2	BCM_SSAHASNP	ss10343494	Jul 11, 2003 (117)
3	ABI	ss42808375	Mar 15, 2006 (126)
4	HUMANGENOME_JCVI	ss98489896	Feb 04, 2009 (130)
5	ENSEMBL	ss143404783	Dec 01, 2009 (131)
6	GMI	ss278751421	May 04, 2012 (137)
7	PJP	ss293836048	May 09, 2011 (134)
8	1000GENOMES	ss333204039	May 09, 2011 (134)
9	TISHKOFF	ss559133952	Apr 25, 2013 (138)
10	SSMP	ss653069274	Apr 25, 2013 (138)
11	EVA-GONL	ss982809019	Aug 21, 2014 (142)
12	JMKIDD_LAB	ss1073527127	Aug 21, 2014 (142)
13	1000GENOMES	ss1319664781	Aug 21, 2014 (142)
14	DDI	ss1430686552	Apr 01, 2015 (144)
15	EVA_GENOME_DK	ss1581625022	Apr 01, 2015 (144)
16	EVA_DECODE	ss1592341995	Apr 01, 2015 (144)
17	EVA_UK10K_ALSPAC	ss1615328600	Apr 01, 2015 (144)
18	EVA_UK10K_TWINSUK	ss1658322633	Apr 01, 2015 (144)
19	HAMMER_LAB	ss1804377542	Sep 08, 2015 (146)
20	WEILL_CORNELL_DGM	ss1926066236	Feb 12, 2016 (147)
21	JJLAB	ss2023670250	Sep 14, 2016 (149)
22	USC_VALOUEV	ss2151847610	Dec 20, 2016 (150)
23	HUMAN_LONGEVITY	ss2283119899	Dec 20, 2016 (150)
24	SYSTEMSBIOZJU	ss2626323441	Nov 08, 2017 (151)
25	GRF	ss2707443320	Nov 08, 2017 (151)
26	GNOMAD	ss2837696856	Nov 08, 2017 (151)
27	SWEGEN	ss2998876556	Nov 08, 2017 (151)
28	CSHL	ss3346908899	Nov 08, 2017 (151)
29	URBANLAB	ss3648327206	Oct 12, 2018 (152)
30	EGCUT_WGS	ss3666763243	Jul 13, 2019 (153)
31	EVA_DECODE	ss3716979649	Jul 13, 2019 (153)
32	ACPOP	ss3733402171	Jul 13, 2019 (153)
33	EVA	ss3764874441	Jul 13, 2019 (153)
34	KHV_HUMAN_GENOMES	ss3808028100	Jul 13, 2019 (153)
35	SGDP_PRJ	ss3864342489	Apr 26, 2020 (154)
36	KRGDB	ss3911125697	Apr 26, 2020 (154)
37	TOPMED	ss4699075958	Apr 26, 2021 (155)
38	TOMMO_GENOMICS	ss5176988031	Apr 26, 2021 (155)
39	1000G_HIGH_COVERAGE	ss5268036291	Oct 13, 2022 (156)
40	EVA	ss5364881401	Oct 13, 2022 (156)
41	HUGCELL_USP	ss5465749374	Oct 13, 2022 (156)
42	EVA	ss5508449269	Oct 13, 2022 (156)
43	1000G_HIGH_COVERAGE	ss5553734453	Oct 13, 2022 (156)
44	SANFORD_IMAGENETICS	ss5640169401	Oct 13, 2022 (156)
45	TOMMO_GENOMICS	ss5714882301	Oct 13, 2022 (156)
46	YY_MCH	ss5807366334	Oct 13, 2022 (156)
47	EVA	ss5842079826	Oct 13, 2022 (156)
48	EVA	ss5855308432	Oct 13, 2022 (156)
49	EVA	ss5883345452	Oct 13, 2022 (156)
50	EVA	ss5968658097	Oct 13, 2022 (156)
51	1000Genomes	NC_000006.11 - 34853891	Oct 12, 2018 (152)
52	1000Genomes_30x	NC_000006.12 - 34886114	Oct 13, 2022 (156)
53	The Avon Longitudinal Study of Parents and Children	NC_000006.11 - 34853891	Oct 12, 2018 (152)
54	Genetic variation in the Estonian population	NC_000006.11 - 34853891	Oct 12, 2018 (152)
55	The Danish reference pan genome	NC_000006.11 - 34853891	Apr 26, 2020 (154)
56	gnomAD - Genomes Submission ignored due to conflicting rows: Row 221873824 (NC_000006.12:34886113:C:A 0/140098) Row 221873825 (NC_000006.12:34886113:C:G 1/140098) Row 221873826 (NC_000006.12:34886113:C:T 9708/140064)	-	Apr 26, 2021 (155)
57	gnomAD - Genomes Submission ignored due to conflicting rows: Row 221873824 (NC_000006.12:34886113:C:A 0/140098) Row 221873825 (NC_000006.12:34886113:C:G 1/140098) Row 221873826 (NC_000006.12:34886113:C:T 9708/140064)	-	Apr 26, 2021 (155)
58	gnomAD - Genomes Submission ignored due to conflicting rows: Row 221873824 (NC_000006.12:34886113:C:A 0/140098) Row 221873825 (NC_000006.12:34886113:C:G 1/140098) Row 221873826 (NC_000006.12:34886113:C:T 9708/140064)	-	Apr 26, 2021 (155)
59	Genome of the Netherlands Release 5	NC_000006.11 - 34853891	Apr 26, 2020 (154)
60	KOREAN population from KRGDB	NC_000006.11 - 34853891	Apr 26, 2020 (154)
61	Northern Sweden	NC_000006.11 - 34853891	Jul 13, 2019 (153)
62	Qatari	NC_000006.11 - 34853891	Apr 26, 2020 (154)
63	SGDP_PRJ	NC_000006.11 - 34853891	Apr 26, 2020 (154)
64	Siberian	NC_000006.11 - 34853891	Apr 26, 2020 (154)
65	8.3KJPN	NC_000006.11 - 34853891	Apr 26, 2021 (155)
66	14KJPN	NC_000006.12 - 34886114	Oct 13, 2022 (156)
67	TopMed	NC_000006.12 - 34886114	Apr 26, 2021 (155)
68	UK 10K study - Twins	NC_000006.11 - 34853891	Oct 12, 2018 (152)
69	ALFA	NC_000006.12 - 34886114	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)
rs6939060	Aug 27, 2003 (117)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
7232494341	NC_000006.12:34886113:C:A	NC_000006.12:34886113:C:A	(self)
7232494341	NC_000006.12:34886113:C:G	NC_000006.12:34886113:C:G	(self)
ss278751421, ss293836048, ss1592341995	NC_000006.10:34961868:C:T	NC_000006.12:34886113:C:T	(self)
31436424, 17524243, 12501491, 7789961, 7802265, 18303091, 6687036, 8108166, 16359469, 4363964, 34957338, 17524243, ss333204039, ss559133952, ss653069274, ss982809019, ss1073527127, ss1319664781, ss1430686552, ss1581625022, ss1615328600, ss1658322633, ss1804377542, ss1926066236, ss2023670250, ss2151847610, ss2626323441, ss2707443320, ss2837696856, ss2998876556, ss3346908899, ss3666763243, ss3733402171, ss3764874441, ss3864342489, ss3911125697, ss5176988031, ss5364881401, ss5508449269, ss5640169401, ss5842079826, ss5968658097	NC_000006.11:34853890:C:T	NC_000006.12:34886113:C:T	(self)
41260388, 48719405, 536453516, 7232494341, ss2283119899, ss3648327206, ss3716979649, ss3808028100, ss4699075958, ss5268036291, ss5465749374, ss5553734453, ss5714882301, ss5807366334, ss5855308432, ss5883345452	NC_000006.12:34886113:C:T	NC_000006.12:34886113:C:T	(self)
ss10343494	NT_007592.13:25651017:C:T	NC_000006.12:34886113:C:T	(self)
ss6312483, ss42808375, ss98489896, ss143404783	NT_007592.15:34793890:C:T	NC_000006.12:34886113:C: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 rs4646919

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

rs4646919