Name: rs201062773
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.

rs201062773

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr6:116066422-116066434 (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: delAT / dupAT / dupATAT
Variation Type: Indel Insertion and Deletion
Frequency: dupAT=0.02810 (794/28258, 14KJPN)
dupAT=0.01258 (216/17170, ALFA)
dupAT=0.02912 (488/16760, 8.3KJPN) (+ 7 more)
dupAT=0.0831 (416/5008, 1000G)
dupAT=0.0482 (216/4480, Estonian)
dupAT=0.0289 (53/1832, Korea1K)
dupAT=0.047 (47/998, GoNL)
dupAT=0.047 (28/600, NorthernSweden)
dupAT=0.028 (6/216, Vietnamese)
dupAT=0.05 (2/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: FRK : 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: 20231103111315

Population	Group	Sample Size	Ref Allele	Alt Allele	Ref HMOZ	Alt HMOZ	HTRZ	HWEP
Total	Global	17170	TATATATATATAT=0.98742	TATATATATAT=0.00000, TATATATATATATAT=0.01258, TATATATATATATATAT=0.00000	0.975655	0.000815	0.023529	13
European	Sub	13624	TATATATATATAT=0.98415	TATATATATAT=0.00000, TATATATATATATAT=0.01585, TATATATATATATATAT=0.00000	0.969319	0.001028	0.029654	10
African	Sub	2484	TATATATATATAT=1.0000	TATATATATAT=0.0000, TATATATATATATAT=0.0000, TATATATATATATATAT=0.0000	1.0	0.0	0.0	N/A
African Others	Sub	82	TATATATATATAT=1.00	TATATATATAT=0.00, TATATATATATATAT=0.00, TATATATATATATATAT=0.00	1.0	0.0	0.0	N/A
African American	Sub	2402	TATATATATATAT=1.0000	TATATATATAT=0.0000, TATATATATATATAT=0.0000, TATATATATATATATAT=0.0000	1.0	0.0	0.0	N/A
Asian	Sub	108	TATATATATATAT=1.000	TATATATATAT=0.000, TATATATATATATAT=0.000, TATATATATATATATAT=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	84	TATATATATATAT=1.00	TATATATATAT=0.00, TATATATATATATAT=0.00, TATATATATATATATAT=0.00	1.0	0.0	0.0	N/A
Other Asian	Sub	24	TATATATATATAT=1.00	TATATATATAT=0.00, TATATATATATATAT=0.00, TATATATATATATATAT=0.00	1.0	0.0	0.0	N/A
Latin American 1	Sub	118	TATATATATATAT=1.000	TATATATATAT=0.000, TATATATATATATAT=0.000, TATATATATATATATAT=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	312	TATATATATATAT=1.000	TATATATATAT=0.000, TATATATATATATAT=0.000, TATATATATATATATAT=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	94	TATATATATATAT=1.00	TATATATATAT=0.00, TATATATATATATAT=0.00, TATATATATATATATAT=0.00	1.0	0.0	0.0	N/A
Other	Sub	430	TATATATATATAT=1.000	TATATATATAT=0.000, TATATATATATATAT=0.000, TATATATATATATATAT=0.000	1.0	0.0	0.0	N/A

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
14KJPN	JAPANESE	Study-wide	28258	- No frequency provided	dupAT=0.02810
Allele Frequency Aggregator	Total	Global	17170	(TA)₆T=0.98742	delAT=0.00000, dupAT=0.01258, dupATAT=0.00000
Allele Frequency Aggregator	European	Sub	13624	(TA)₆T=0.98415	delAT=0.00000, dupAT=0.01585, dupATAT=0.00000
Allele Frequency Aggregator	African	Sub	2484	(TA)₆T=1.0000	delAT=0.0000, dupAT=0.0000, dupATAT=0.0000
Allele Frequency Aggregator	Other	Sub	430	(TA)₆T=1.000	delAT=0.000, dupAT=0.000, dupATAT=0.000
Allele Frequency Aggregator	Latin American 2	Sub	312	(TA)₆T=1.000	delAT=0.000, dupAT=0.000, dupATAT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	118	(TA)₆T=1.000	delAT=0.000, dupAT=0.000, dupATAT=0.000
Allele Frequency Aggregator	Asian	Sub	108	(TA)₆T=1.000	delAT=0.000, dupAT=0.000, dupATAT=0.000
Allele Frequency Aggregator	South Asian	Sub	94	(TA)₆T=1.00	delAT=0.00, dupAT=0.00, dupATAT=0.00
8.3KJPN	JAPANESE	Study-wide	16760	- No frequency provided	dupAT=0.02912
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupAT=0.0831
1000Genomes	African	Sub	1322	- No frequency provided	dupAT=0.0832
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupAT=0.0298
1000Genomes	Europe	Sub	1006	- No frequency provided	dupAT=0.0477
1000Genomes	South Asian	Sub	978	- No frequency provided	dupAT=0.080
1000Genomes	American	Sub	694	- No frequency provided	dupAT=0.216
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	dupAT=0.0482
Korean Genome Project	KOREAN	Study-wide	1832	- No frequency provided	dupAT=0.0289
Genome of the Netherlands Release 5	Genome of the Netherlands	Study-wide	998	- No frequency provided	dupAT=0.047
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupAT=0.047
A Vietnamese Genetic Variation Database	Global	Study-wide	216	- No frequency provided	dupAT=0.028
The Danish reference pan genome	Danish	Study-wide	40	- No frequency provided	dupAT=0.05

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.116066423AT[5]
GRCh38.p14 chr 6	NC_000006.12:g.116066423AT[7]
GRCh38.p14 chr 6	NC_000006.12:g.116066423AT[8]
GRCh37.p13 chr 6	NC_000006.11:g.116387586AT[5]
GRCh37.p13 chr 6	NC_000006.11:g.116387586AT[7]
GRCh37.p13 chr 6	NC_000006.11:g.116387586AT[8]

Gene: FRK, fyn related Src family tyrosine kinase (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
FRK transcript	NM_002031.3:c.	N/A	Genic Upstream Transcript Variant
FRK transcript variant X7	XM_011535654.3:c.-286-583… XM_011535654.3:c.-286-5836TA[5]	N/A	Intron Variant
FRK transcript variant X6	XM_011535655.3:c.-283-583… XM_011535655.3:c.-283-5839TA[5]	N/A	Intron Variant
FRK transcript variant X8	XM_011535656.3:c.5+34059T… XM_011535656.3:c.5+34059TA[5]	N/A	Intron Variant
FRK transcript variant X2	XM_047418554.1:c.-283-583… XM_047418554.1:c.-283-5839TA[5]	N/A	Intron Variant
FRK transcript variant X5	XM_047418555.1:c.-286-583… XM_047418555.1:c.-286-5836TA[5]	N/A	Intron Variant
FRK transcript variant X1	XM_005266880.5:c.	N/A	Genic Upstream Transcript Variant
FRK transcript variant X4	XM_005266881.3:c.	N/A	Genic Upstream Transcript Variant
FRK transcript variant X3	XM_017010645.2: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	(TA)₆T=	delAT	dupAT	dupATAT
GRCh38.p14 chr 6	NC_000006.12:g.116066422_116066434=	NC_000006.12:g.116066423AT[5]	NC_000006.12:g.116066423AT[7]	NC_000006.12:g.116066423AT[8]
GRCh37.p13 chr 6	NC_000006.11:g.116387585_116387597=	NC_000006.11:g.116387586AT[5]	NC_000006.11:g.116387586AT[7]	NC_000006.11:g.116387586AT[8]
FRK transcript variant X3	XM_005266882.1:c.-283-5828=	XM_005266882.1:c.-283-5839TA[5]	XM_005266882.1:c.-283-5839TA[7]	XM_005266882.1:c.-283-5839TA[8]
FRK transcript variant X7	XM_011535654.3:c.-286-5825=	XM_011535654.3:c.-286-5836TA[5]	XM_011535654.3:c.-286-5836TA[7]	XM_011535654.3:c.-286-5836TA[8]
FRK transcript variant X6	XM_011535655.3:c.-283-5828=	XM_011535655.3:c.-283-5839TA[5]	XM_011535655.3:c.-283-5839TA[7]	XM_011535655.3:c.-283-5839TA[8]
FRK transcript variant X8	XM_011535656.3:c.5+34070=	XM_011535656.3:c.5+34059TA[5]	XM_011535656.3:c.5+34059TA[7]	XM_011535656.3:c.5+34059TA[8]
FRK transcript variant X2	XM_047418554.1:c.-283-5828=	XM_047418554.1:c.-283-5839TA[5]	XM_047418554.1:c.-283-5839TA[7]	XM_047418554.1:c.-283-5839TA[8]
FRK transcript variant X5	XM_047418555.1:c.-286-5825=	XM_047418555.1:c.-286-5836TA[5]	XM_047418555.1:c.-286-5836TA[7]	XM_047418555.1:c.-286-5836TA[8]

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#.

36 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	GMI	ss288795586	May 04, 2012 (137)
2	LUNTER	ss551656681	Apr 25, 2013 (138)
3	LUNTER	ss551848861	Apr 25, 2013 (138)
4	SSMP	ss663644323	Apr 01, 2015 (144)
5	SSIP	ss947178866	Aug 21, 2014 (142)
6	EVA-GONL	ss983405694	Aug 21, 2014 (142)
7	1000GENOMES	ss1376047756	Aug 21, 2014 (142)
8	EVA_GENOME_DK	ss1576841367	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1705331363	Jan 10, 2018 (151)
10	EVA_UK10K_TWINSUK	ss1705331623	Jan 10, 2018 (151)
11	EVA_UK10K_ALSPAC	ss1710289812	Apr 01, 2015 (144)
12	EVA_UK10K_TWINSUK	ss1710289816	Apr 01, 2015 (144)
13	JJLAB	ss2030790596	Sep 14, 2016 (149)
14	SWEGEN	ss2999808867	Nov 08, 2017 (151)
15	EGCUT_WGS	ss3667710446	Jul 13, 2019 (153)
16	EVA_DECODE	ss3718103269	Jul 13, 2019 (153)
17	EVA_DECODE	ss3718103270	Jul 13, 2019 (153)
18	EVA_DECODE	ss3718103271	Jul 13, 2019 (153)
19	ACPOP	ss3733904128	Jul 13, 2019 (153)
20	KHV_HUMAN_GENOMES	ss3808715783	Jul 13, 2019 (153)
21	EVA	ss3830151228	Apr 26, 2020 (154)
22	EVA	ss3838558697	Apr 26, 2020 (154)
23	EVA	ss3844008170	Apr 26, 2020 (154)
24	KOGIC	ss3959913056	Apr 26, 2020 (154)
25	GNOMAD	ss4149838634	Apr 26, 2021 (155)
26	GNOMAD	ss4149838635	Apr 26, 2021 (155)
27	GNOMAD	ss4149838636	Apr 26, 2021 (155)
28	TOMMO_GENOMICS	ss5179530037	Apr 26, 2021 (155)
29	1000G_HIGH_COVERAGE	ss5270037166	Oct 13, 2022 (156)
30	HUGCELL_USP	ss5467508539	Oct 13, 2022 (156)
31	EVA	ss5508676120	Oct 13, 2022 (156)
32	SANFORD_IMAGENETICS	ss5641311771	Oct 13, 2022 (156)
33	TOMMO_GENOMICS	ss5718305174	Oct 13, 2022 (156)
34	YY_MCH	ss5807879964	Oct 13, 2022 (156)
35	EVA	ss5842866932	Oct 13, 2022 (156)
36	EVA	ss5842866933	Oct 13, 2022 (156)
37	1000Genomes	NC_000006.11 - 116387585	Oct 12, 2018 (152)
38	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 18818582 (NC_000006.11:116387584:TA: 89/3854) Row 18818583 (NC_000006.11:116387584::TA 154/3854)	-	Oct 12, 2018 (152)
39	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 18818582 (NC_000006.11:116387584:TA: 89/3854) Row 18818583 (NC_000006.11:116387584::TA 154/3854)	-	Oct 12, 2018 (152)
40	Genetic variation in the Estonian population	NC_000006.11 - 116387585	Oct 12, 2018 (152)
41	The Danish reference pan genome	NC_000006.11 - 116387585	Apr 26, 2020 (154)
42	gnomAD - Genomes Submission ignored due to conflicting rows: Row 238482299 (NC_000006.12:116066421::TA 9644/139102) Row 238482300 (NC_000006.12:116066421::TATA 3/139172) Row 238482301 (NC_000006.12:116066421:TA: 26/139170)	-	Apr 26, 2021 (155)
43	gnomAD - Genomes Submission ignored due to conflicting rows: Row 238482299 (NC_000006.12:116066421::TA 9644/139102) Row 238482300 (NC_000006.12:116066421::TATA 3/139172) Row 238482301 (NC_000006.12:116066421:TA: 26/139170)	-	Apr 26, 2021 (155)
44	gnomAD - Genomes Submission ignored due to conflicting rows: Row 238482299 (NC_000006.12:116066421::TA 9644/139102) Row 238482300 (NC_000006.12:116066421::TATA 3/139172) Row 238482301 (NC_000006.12:116066421:TA: 26/139170)	-	Apr 26, 2021 (155)
45	Genome of the Netherlands Release 5	NC_000006.11 - 116387585	Apr 26, 2020 (154)
46	Korean Genome Project	NC_000006.12 - 116066422	Apr 26, 2020 (154)
47	Northern Sweden	NC_000006.11 - 116387585	Jul 13, 2019 (153)
48	8.3KJPN	NC_000006.11 - 116387585	Apr 26, 2021 (155)
49	14KJPN	NC_000006.12 - 116066422	Oct 13, 2022 (156)
50	UK 10K study - Twins Submission ignored due to conflicting rows: Row 18818582 (NC_000006.11:116387584:TA: 78/3708) Row 18818583 (NC_000006.11:116387584::TA 141/3708)	-	Oct 12, 2018 (152)
51	UK 10K study - Twins Submission ignored due to conflicting rows: Row 18818582 (NC_000006.11:116387584:TA: 78/3708) Row 18818583 (NC_000006.11:116387584::TA 141/3708)	-	Oct 12, 2018 (152)
52	A Vietnamese Genetic Variation Database	NC_000006.11 - 116387585	Jul 13, 2019 (153)
53	ALFA	NC_000006.12 - 116066422	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)
rs375078775	May 15, 2013 (138)
rs796825640	Nov 08, 2017 (151)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1705331363, ss1705331623, ss5508676120, ss5842866933	NC_000006.11:116387584:TA:	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATAT	(self)
ss3718103269, ss4149838636	NC_000006.12:116066421:TA:	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATAT	(self)
6612281739	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATAT	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATAT	(self)
ss551656681, ss551848861	NC_000006.10:116494277::TA	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATATATAT	(self)
ss288795586	NC_000006.10:116494290::AT	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATATATAT	(self)
33770341, 13448694, 1102978, 8382434, 7188993, 37499344, 4185885, ss663644323, ss947178866, ss983405694, ss1376047756, ss1576841367, ss2030790596, ss2999808867, ss3667710446, ss3733904128, ss3830151228, ss3838558697, ss5179530037, ss5641311771, ss5842866932	NC_000006.11:116387584::TA	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATATATAT	(self)
ss1710289812, ss1710289816	NC_000006.11:116387586::TA	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATATATAT	(self)
16291057, 52142278, ss3808715783, ss3844008170, ss3959913056, ss4149838634, ss5270037166, ss5467508539, ss5718305174, ss5807879964	NC_000006.12:116066421::TA	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATATATAT	(self)
6612281739	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATATATAT	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATATATAT	(self)
ss3718103270	NC_000006.12:116066423::TA	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATATATAT	(self)
ss4149838635	NC_000006.12:116066421::TATA	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATATATATAT	(self)
6612281739	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATATATATAT	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATATATATAT	(self)
ss3718103271	NC_000006.12:116066423::TATA	NC_000006.12:116066421:TATATATATAT… NC_000006.12:116066421:TATATATATATAT:TATATATATATATATAT	(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 rs201062773

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
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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

rs201062773