Name: rs71563939
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.

rs71563939

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chr7:44210723-44210735 (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: delAT=0.000023 (6/264690, TOPMED)
dupAT=0.06929 (1958/28258, 14KJPN)
dupAT=0.01774 (322/18148, ALFA) (+ 5 more)
dupAT=0.07000 (1173/16758, 8.3KJPN)
dupAT=0.0451 (226/5008, 1000G)
dupAT=0.0719 (322/4480, Estonian)
dupAT=0.048 (29/600, NorthernSweden)
dupAT=0.05 (2/40, GENOME_DK)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: YKT6 : 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	18148	TATATATATATAT=0.98226	TATATATATAT=0.00000, TATATATATATATAT=0.01774, TATATATATATATATAT=0.00000	0.966277	0.001763	0.031959	33
European	Sub	13836	TATATATATATAT=0.97673	TATATATATAT=0.00000, TATATATATATATAT=0.02327, TATATATATATATATAT=0.00000	0.955768	0.002313	0.04192	23
African	Sub	2880	TATATATATATAT=1.0000	TATATATATAT=0.0000, TATATATATATATAT=0.0000, TATATATATATATATAT=0.0000	1.0	0.0	0.0	N/A
African Others	Sub	114	TATATATATATAT=1.000	TATATATATAT=0.000, TATATATATATATAT=0.000, TATATATATATATATAT=0.000	1.0	0.0	0.0	N/A
African American	Sub	2766	TATATATATATAT=1.0000	TATATATATAT=0.0000, TATATATATATATAT=0.0000, TATATATATATATATAT=0.0000	1.0	0.0	0.0	N/A
Asian	Sub	102	TATATATATATAT=1.000	TATATATATAT=0.000, TATATATATATATAT=0.000, TATATATATATATATAT=0.000	1.0	0.0	0.0	N/A
East Asian	Sub	78	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	142	TATATATATATAT=1.000	TATATATATAT=0.000, TATATATATATATAT=0.000, TATATATATATATATAT=0.000	1.0	0.0	0.0	N/A
Latin American 2	Sub	598	TATATATATATAT=1.000	TATATATATAT=0.000, TATATATATATATAT=0.000, TATATATATATATATAT=0.000	1.0	0.0	0.0	N/A
South Asian	Sub	96	TATATATATATAT=1.00	TATATATATAT=0.00, TATATATATATATAT=0.00, TATATATATATATATAT=0.00	1.0	0.0	0.0	N/A
Other	Sub	494	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
TopMed	Global	Study-wide	264690	(TA)₆T=0.999977	delAT=0.000023
14KJPN	JAPANESE	Study-wide	28258	- No frequency provided	dupAT=0.06929
Allele Frequency Aggregator	Total	Global	18148	(TA)₆T=0.98226	delAT=0.00000, dupAT=0.01774, dupATAT=0.00000
Allele Frequency Aggregator	European	Sub	13836	(TA)₆T=0.97673	delAT=0.00000, dupAT=0.02327, dupATAT=0.00000
Allele Frequency Aggregator	African	Sub	2880	(TA)₆T=1.0000	delAT=0.0000, dupAT=0.0000, dupATAT=0.0000
Allele Frequency Aggregator	Latin American 2	Sub	598	(TA)₆T=1.000	delAT=0.000, dupAT=0.000, dupATAT=0.000
Allele Frequency Aggregator	Other	Sub	494	(TA)₆T=1.000	delAT=0.000, dupAT=0.000, dupATAT=0.000
Allele Frequency Aggregator	Latin American 1	Sub	142	(TA)₆T=1.000	delAT=0.000, dupAT=0.000, dupATAT=0.000
Allele Frequency Aggregator	Asian	Sub	102	(TA)₆T=1.000	delAT=0.000, dupAT=0.000, dupATAT=0.000
Allele Frequency Aggregator	South Asian	Sub	96	(TA)₆T=1.00	delAT=0.00, dupAT=0.00, dupATAT=0.00
8.3KJPN	JAPANESE	Study-wide	16758	- No frequency provided	dupAT=0.07000
1000Genomes	Global	Study-wide	5008	- No frequency provided	dupAT=0.0451
1000Genomes	African	Sub	1322	- No frequency provided	dupAT=0.0068
1000Genomes	East Asian	Sub	1008	- No frequency provided	dupAT=0.0685
1000Genomes	Europe	Sub	1006	- No frequency provided	dupAT=0.0636
1000Genomes	South Asian	Sub	978	- No frequency provided	dupAT=0.054
1000Genomes	American	Sub	694	- No frequency provided	dupAT=0.045
Genetic variation in the Estonian population	Estonian	Study-wide	4480	- No frequency provided	dupAT=0.0719
Northern Sweden	ACPOP	Study-wide	600	- No frequency provided	dupAT=0.048
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 7	NC_000007.14:g.44210724AT[5]
GRCh38.p14 chr 7	NC_000007.14:g.44210724AT[7]
GRCh38.p14 chr 7	NC_000007.14:g.44210724AT[8]
GRCh37.p13 chr 7	NC_000007.13:g.44250323AT[5]
GRCh37.p13 chr 7	NC_000007.13:g.44250323AT[7]
GRCh37.p13 chr 7	NC_000007.13:g.44250323AT[8]

Gene: YKT6, YKT6 v-SNARE homolog (plus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
YKT6 transcript variant 2	NM_001363678.2:c.460-1524… NM_001363678.2:c.460-1524TA[5]	N/A	Intron Variant
YKT6 transcript variant 1	NM_006555.4:c.460-300TA[5]	N/A	Intron Variant
YKT6 transcript variant X1	XM_047419785.1:c.460-300T… XM_047419785.1:c.460-300TA[5]	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	(TA)₆T=	delAT	dupAT	dupATAT
GRCh38.p14 chr 7	NC_000007.14:g.44210723_44210735=	NC_000007.14:g.44210724AT[5]	NC_000007.14:g.44210724AT[7]	NC_000007.14:g.44210724AT[8]
GRCh37.p13 chr 7	NC_000007.13:g.44250322_44250334=	NC_000007.13:g.44250323AT[5]	NC_000007.13:g.44250323AT[7]	NC_000007.13:g.44250323AT[8]
YKT6 transcript variant 2	NM_001363678.2:c.460-1524=	NM_001363678.2:c.460-1524TA[5]	NM_001363678.2:c.460-1524TA[7]	NM_001363678.2:c.460-1524TA[8]
YKT6 transcript variant 1	NM_006555.3:c.460-300=	NM_006555.3:c.460-300TA[5]	NM_006555.3:c.460-300TA[7]	NM_006555.3:c.460-300TA[8]
YKT6 transcript variant 1	NM_006555.4:c.460-300=	NM_006555.4:c.460-300TA[5]	NM_006555.4:c.460-300TA[7]	NM_006555.4:c.460-300TA[8]
YKT6 transcript variant X1	XM_005249582.1:c.460-300=	XM_005249582.1:c.460-300TA[5]	XM_005249582.1:c.460-300TA[7]	XM_005249582.1:c.460-300TA[8]
YKT6 transcript variant X2	XM_005249583.1:c.460-1524=	XM_005249583.1:c.460-1524TA[5]	XM_005249583.1:c.460-1524TA[7]	XM_005249583.1:c.460-1524TA[8]
YKT6 transcript variant X1	XM_047419785.1:c.460-300=	XM_047419785.1:c.460-300TA[5]	XM_047419785.1:c.460-300TA[7]	XM_047419785.1:c.460-300TA[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#.

43 SubSNP, 17 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	HUMANGENOME_JCVI	ss98206784	Feb 13, 2009 (130)
2	GMI	ss288837673	May 04, 2012 (137)
3	1000GENOMES	ss326929462	May 09, 2011 (135)
4	LUNTER	ss551728202	Apr 25, 2013 (138)
5	LUNTER	ss553294913	Apr 25, 2013 (138)
6	SSMP	ss663780087	Apr 01, 2015 (144)
7	1000GENOMES	ss1377034075	Aug 21, 2014 (142)
8	EVA_GENOME_DK	ss1576981537	Apr 01, 2015 (144)
9	EVA_UK10K_ALSPAC	ss1705610256	Jan 10, 2018 (151)
10	EVA_UK10K_TWINSUK	ss1705610663	Jan 10, 2018 (151)
11	EVA_UK10K_ALSPAC	ss1710320973	Apr 01, 2015 (144)
12	EVA_UK10K_TWINSUK	ss1710327339	Apr 01, 2015 (144)
13	JJLAB	ss2030836673	Sep 14, 2016 (149)
14	SWEGEN	ss3001018432	Nov 08, 2017 (151)
15	MCHAISSO	ss3065133520	Nov 08, 2017 (151)
16	URBANLAB	ss3648616385	Oct 12, 2018 (152)
17	EGCUT_WGS	ss3668939836	Jul 13, 2019 (153)
18	EVA_DECODE	ss3719574579	Jul 13, 2019 (153)
19	EVA_DECODE	ss3719574580	Jul 13, 2019 (153)
20	ACPOP	ss3734576306	Jul 13, 2019 (153)
21	KHV_HUMAN_GENOMES	ss3809649489	Jul 13, 2019 (153)
22	EVA	ss3830540899	Apr 26, 2020 (154)
23	KOGIC	ss3961346081	Apr 26, 2020 (154)
24	KOGIC	ss3961346082	Apr 26, 2020 (154)
25	FSA-LAB	ss3984365863	Apr 27, 2021 (155)
26	EVA	ss3986380616	Apr 27, 2021 (155)
27	GNOMAD	ss4162433302	Apr 27, 2021 (155)
28	GNOMAD	ss4162433303	Apr 27, 2021 (155)
29	GNOMAD	ss4162433304	Apr 27, 2021 (155)
30	TOPMED	ss4743895491	Apr 27, 2021 (155)
31	TOMMO_GENOMICS	ss5182881060	Apr 27, 2021 (155)
32	1000G_HIGH_COVERAGE	ss5272665148	Oct 14, 2022 (156)
33	HUGCELL_USP	ss5469861889	Oct 14, 2022 (156)
34	EVA	ss5508933961	Oct 14, 2022 (156)
35	SANFORD_IMAGENETICS	ss5642827851	Oct 14, 2022 (156)
36	TOMMO_GENOMICS	ss5722637057	Oct 14, 2022 (156)
37	YY_MCH	ss5808547440	Oct 14, 2022 (156)
38	EVA	ss5822738503	Oct 14, 2022 (156)
39	EVA	ss5822738504	Oct 14, 2022 (156)
40	EVA	ss5848681348	Oct 14, 2022 (156)
41	EVA	ss5855867650	Oct 14, 2022 (156)
42	EVA	ss5858664031	Oct 14, 2022 (156)
43	EVA	ss5981242355	Oct 14, 2022 (156)
44	1000Genomes	NC_000007.13 - 44250322	Oct 12, 2018 (152)
45	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 20549228 (NC_000007.13:44250321::TA 261/3854) Row 20549229 (NC_000007.13:44250321:TA: 51/3854)	-	Oct 12, 2018 (152)
46	The Avon Longitudinal Study of Parents and Children Submission ignored due to conflicting rows: Row 20549228 (NC_000007.13:44250321::TA 261/3854) Row 20549229 (NC_000007.13:44250321:TA: 51/3854)	-	Oct 12, 2018 (152)
47	Genetic variation in the Estonian population	NC_000007.13 - 44250322	Oct 12, 2018 (152)
48	The Danish reference pan genome	NC_000007.13 - 44250322	Apr 26, 2020 (154)
49	gnomAD - Genomes Submission ignored due to conflicting rows: Row 259763299 (NC_000007.14:44210722::TA 7357/139702) Row 259763300 (NC_000007.14:44210722::TATA 5/139728) Row 259763301 (NC_000007.14:44210722:TA: 3/139702)	-	Apr 27, 2021 (155)
50	gnomAD - Genomes Submission ignored due to conflicting rows: Row 259763299 (NC_000007.14:44210722::TA 7357/139702) Row 259763300 (NC_000007.14:44210722::TATA 5/139728) Row 259763301 (NC_000007.14:44210722:TA: 3/139702)	-	Apr 27, 2021 (155)
51	gnomAD - Genomes Submission ignored due to conflicting rows: Row 259763299 (NC_000007.14:44210722::TA 7357/139702) Row 259763300 (NC_000007.14:44210722::TATA 5/139728) Row 259763301 (NC_000007.14:44210722:TA: 3/139702)	-	Apr 27, 2021 (155)
52	Korean Genome Project Submission ignored due to conflicting rows: Row 17724082 (NC_000007.14:44210724::TA 168/1832) Row 17724083 (NC_000007.14:44210722:TA: 5/1832)	-	Apr 26, 2020 (154)
53	Korean Genome Project Submission ignored due to conflicting rows: Row 17724082 (NC_000007.14:44210724::TA 168/1832) Row 17724083 (NC_000007.14:44210722:TA: 5/1832)	-	Apr 26, 2020 (154)
54	Northern Sweden	NC_000007.13 - 44250322	Jul 13, 2019 (153)
55	8.3KJPN	NC_000007.13 - 44250322	Apr 27, 2021 (155)
56	14KJPN	NC_000007.14 - 44210723	Oct 14, 2022 (156)
57	TopMed	NC_000007.14 - 44210723	Apr 27, 2021 (155)
58	UK 10K study - Twins Submission ignored due to conflicting rows: Row 20549228 (NC_000007.13:44250321::TA 275/3708) Row 20549229 (NC_000007.13:44250321:TA: 30/3708)	-	Oct 12, 2018 (152)
59	UK 10K study - Twins Submission ignored due to conflicting rows: Row 20549228 (NC_000007.13:44250321::TA 275/3708) Row 20549229 (NC_000007.13:44250321:TA: 30/3708)	-	Oct 12, 2018 (152)
60	ALFA	NC_000007.14 - 44210723	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)
rs150524406	Sep 17, 2011 (135)
rs376722167	May 15, 2013 (138)
rs796381869	Nov 08, 2017 (151)

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss1705610256, ss1705610663, ss5508933961, ss5822738504	NC_000007.13:44250321:TA:	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATAT	(self)
581273050, ss3719574579, ss3961346082, ss4162433304, ss4743895491	NC_000007.14:44210722:TA:	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATAT	(self)
9429576144	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATAT	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATAT	(self)
ss326929462, ss551728202, ss553294913	NC_000007.12:44216846::TA	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATATATAT	(self)
ss288837673	NC_000007.12:44216859::AT	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATATATAT	(self)
36847404, 14678084, 1147459, 7861171, 40850367, ss663780087, ss1377034075, ss1576981537, ss2030836673, ss3001018432, ss3668939836, ss3734576306, ss3830540899, ss3984365863, ss3986380616, ss5182881060, ss5642827851, ss5822738503, ss5981242355	NC_000007.13:44250321::TA	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATATATAT	(self)
ss1710320973, ss1710327339	NC_000007.13:44250323::TA	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATATATAT	(self)
ss5848681348	NC_000007.13:44250334::AT	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATATATAT
56474161, ss3065133520, ss3648616385, ss3809649489, ss4162433302, ss5272665148, ss5469861889, ss5722637057, ss5808547440, ss5855867650, ss5858664031	NC_000007.14:44210722::TA	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATATATAT	(self)
9429576144	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATATATAT	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATATATAT	(self)
ss3719574580, ss3961346081	NC_000007.14:44210724::TA	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATATATAT	(self)
ss98206784	NT_007819.17:44240321::TA	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATATATAT	(self)
ss4162433303	NC_000007.14:44210722::TATA	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATATATATAT	(self)
9429576144	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722:TATATATATATAT:TATATATATATATATAT	NC_000007.14:44210722:TATATATATATA… NC_000007.14:44210722: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 rs71563939

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

rs71563939