Name: rs6530602
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.

rs6530602

Current Build 156

Released September 21, 2022

Organism: Homo sapiens
Position: chrY:18991723 (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>C / T>G
Variation Type: SNV Single Nucleotide Variation
Frequency: T=0.2379 (697/2930, KOREAN)
T=0.2483 (356/1434, ALFA)
T=0.312 (174/558, SGDP_PRJ) (+ 3 more)
T=0.29 (16/56, Siberian)
T=0.25 (10/40, GENOME_DK)
C=0.3 (1/3, Vietnamese)

Clinical Significance: Not Reported in ClinVar
Gene : Consequence: TTTY14 : 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	1434	T=0.2483	C=0.7517
European	Sub	1218	T=0.2570	C=0.7430
African	Sub	76	T=0.16	C=0.84
African Others	Sub	4	T=0.0	C=1.0
African American	Sub	72	T=0.17	C=0.83
Asian	Sub	8	T=0.1	C=0.9
East Asian	Sub	8	T=0.1	C=0.9
Other Asian	Sub	0	T=0	C=0
Latin American 1	Sub	2	T=0.5	C=0.5
Latin American 2	Sub	12	T=0.17	C=0.83
South Asian	Sub	0	T=0	C=0
Other	Sub	118	T=0.229	C=0.771

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
KOREAN population from KRGDB	KOREAN	Study-wide	2930	T=0.2379	C=0.7621
Allele Frequency Aggregator	Total	Global	1434	T=0.2483	C=0.7517
Allele Frequency Aggregator	European	Sub	1218	T=0.2570	C=0.7430
Allele Frequency Aggregator	Other	Sub	118	T=0.229	C=0.771
Allele Frequency Aggregator	African	Sub	76	T=0.16	C=0.84
Allele Frequency Aggregator	Latin American 2	Sub	12	T=0.17	C=0.83
Allele Frequency Aggregator	Asian	Sub	8	T=0.1	C=0.9
Allele Frequency Aggregator	Latin American 1	Sub	2	T=0.5	C=0.5
Allele Frequency Aggregator	South Asian	Sub	0	T=0	C=0
SGDP_PRJ	Global	Study-wide	558	T=0.312	C=0.688
Siberian	Global	Study-wide	56	T=0.29	C=0.71
The Danish reference pan genome	Danish	Study-wide	40	T=0.25	C=0.75
A Vietnamese Genetic Variation Database	Global	Study-wide	3	T=0.7	C=0.3

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 Y	NC_000024.10:g.18991723T>C
GRCh38.p14 chr Y	NC_000024.10:g.18991723T>G
GRCh37.p13 chr Y	NC_000024.9:g.21153609T>C
GRCh37.p13 chr Y	NC_000024.9:g.21153609T>G
CD24P4 pseudogene	NG_006012.6:g.1196A>G
CD24P4 pseudogene	NG_006012.6:g.1196A>C

Gene: TTTY14, testis-specific transcript, Y-linked 14 (minus strand)

Molecule type	Change	Amino acid[Codon]	SO Term
TTTY14 transcript variant 5	NR_001543.4:n.	N/A	Intron Variant
TTTY14 transcript variant 1	NR_125733.1:n.	N/A	Intron Variant
TTTY14 transcript variant 2	NR_125734.1:n.	N/A	Intron Variant
TTTY14 transcript variant 3	NR_125735.1:n.	N/A	Intron Variant
TTTY14 transcript variant 4	NR_125736.1:n.	N/A	Intron Variant
TTTY14 transcript variant 6	NR_125737.2:n.	N/A	Intron Variant
TTTY14 transcript variant 7	NR_158640.1:n.	N/A	Intron Variant
TTTY14 transcript variant 8	NR_158641.1:n.	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=	C	G
GRCh38.p14 chr Y	NC_000024.10:g.18991723=	NC_000024.10:g.18991723T>C	NC_000024.10:g.18991723T>G
GRCh37.p13 chr Y	NC_000024.9:g.21153609=	NC_000024.9:g.21153609T>C	NC_000024.9:g.21153609T>G
CD24P4 pseudogene	NG_006012.6:g.1196=	NG_006012.6:g.1196A>G	NG_006012.6:g.1196A>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#.

53 SubSNP, 6 Frequency submissions

No	Submitter	Submission ID	Date (Build)
1	BCM_SSAHASNP	ss10580816	Jul 11, 2003 (116)
2	WI_SSAHASNP	ss12058302	Jul 11, 2003 (116)
3	SC_SNP	ss14801451	Dec 05, 2003 (119)
4	CSHL-HAPMAP	ss18052487	Feb 27, 2004 (120)
5	CSHL-HAPMAP	ss19825364	Feb 27, 2004 (120)
6	SSAHASNP	ss22884070	Apr 05, 2004 (121)
7	ABI	ss43980591	Mar 14, 2006 (126)
8	HGSV	ss77321549	Dec 06, 2007 (129)
9	HGSV	ss78199983	Dec 06, 2007 (129)
10	HGSV	ss78832503	Dec 06, 2007 (129)
11	BCMHGSC_JDW	ss94450263	Mar 25, 2008 (129)
12	BGI	ss105778606	Feb 05, 2009 (130)
13	ENSEMBL	ss133743876	Dec 01, 2009 (131)
14	ENSEMBL	ss144449620	Dec 01, 2009 (131)
15	GMI	ss157863181	Dec 01, 2009 (131)
16	ILLUMINA	ss159849425	Dec 01, 2009 (131)
17	COMPLETE_GENOMICS	ss166083350	Jul 04, 2010 (132)
18	ILLUMINA	ss169061376	Jul 04, 2010 (132)
19	BUSHMAN	ss204419059	Jul 04, 2010 (132)
20	BCM-HGSC-SUB	ss208946314	Jul 04, 2010 (132)
21	GMI	ss283923854	May 04, 2012 (137)
22	GMI	ss287666159	Apr 25, 2013 (138)
23	PJP	ss294561961	May 09, 2011 (134)
24	ILLUMINA	ss479152841	May 04, 2012 (137)
25	ILLUMINA	ss479153150	May 04, 2012 (137)
26	ILLUMINA	ss479157785	Sep 08, 2015 (146)
27	TISHKOFF	ss567116029	Apr 25, 2013 (138)
28	ILLUMINA	ss778657827	Aug 21, 2014 (142)
29	ILLUMINA	ss780910170	Aug 21, 2014 (142)
30	ILLUMINA	ss834115931	Aug 21, 2014 (142)
31	DDI	ss1432160898	Apr 01, 2015 (144)
32	EVA_GENOME_DK	ss1583556554	Apr 01, 2015 (144)
33	ILLUMINA	ss1958180145	Feb 12, 2016 (147)
34	USC_VALOUEV	ss2159356839	Dec 20, 2016 (150)
35	SYSTEMSBIOZJU	ss2629805515	Nov 08, 2017 (151)
36	ILLUMINA	ss2634994540	Nov 08, 2017 (151)
37	GRF	ss2710441118	Nov 08, 2017 (151)
38	SWEGEN	ss3020960292	Nov 08, 2017 (151)
39	ILLUMINA	ss3023054654	Nov 08, 2017 (151)
40	ILLUMINA	ss3632877428	Oct 12, 2018 (152)
41	ILLUMINA	ss3637015397	Oct 12, 2018 (152)
42	ILLUMINA	ss3638887285	Oct 12, 2018 (152)
43	ILLUMINA	ss3641565446	Oct 12, 2018 (152)
44	ILLUMINA	ss3642746551	Oct 12, 2018 (152)
45	OMUKHERJEE_ADBS	ss3646579478	Oct 12, 2018 (152)
46	ILLUMINA	ss3653613252	Oct 12, 2018 (152)
47	EVA	ss3836375068	Apr 27, 2020 (154)
48	SGDP_PRJ	ss3892746061	Apr 27, 2020 (154)
49	KRGDB	ss3943534143	Apr 27, 2020 (154)
50	FSA-LAB	ss3984446685	Apr 27, 2021 (155)
51	EVA	ss3986090464	Apr 27, 2021 (155)
52	SANFORD_IMAGENETICS	ss5666143608	Oct 13, 2022 (156)
53	YY_MCH	ss5819520752	Oct 13, 2022 (156)
54	The Danish reference pan genome	NC_000024.9 - 21153609	Apr 27, 2020 (154)
55	KOREAN population from KRGDB	NC_000024.9 - 21153609	Apr 27, 2020 (154)
56	SGDP_PRJ	NC_000024.9 - 21153609	Apr 27, 2020 (154)
57	Siberian	NC_000024.9 - 21153609	Apr 27, 2020 (154)
58	A Vietnamese Genetic Variation Database	NC_000024.9 - 21153609	Jul 14, 2019 (153)
59	ALFA	NC_000024.10 - 18991723	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).

Added to this RefSNP Cluster:

Submission IDs	Observation SPDI	Canonical SPDI	Source RSIDs
ss77321549, ss78199983, ss78832503	NC_000024.7:19541733:T:C	NC_000024.10:18991722:T:C	(self)
ss94450263, ss159849425, ss166083350, ss204419059, ss208946314, ss283923854, ss287666159, ss294561961, ss479152841	NC_000024.8:19612996:T:C	NC_000024.10:18991722:T:C	(self)
9721491, 50711537, 44763041, 11873193, 10243641, ss479153150, ss479157785, ss567116029, ss778657827, ss780910170, ss834115931, ss1432160898, ss1583556554, ss1958180145, ss2159356839, ss2629805515, ss2634994540, ss2710441118, ss3020960292, ss3023054654, ss3632877428, ss3637015397, ss3638887285, ss3641565446, ss3642746551, ss3646579478, ss3653613252, ss3836375068, ss3892746061, ss3943534143, ss3984446685, ss3986090464, ss5666143608	NC_000024.9:21153608:T:C	NC_000024.10:18991722:T:C	(self)
12653707553, ss5819520752	NC_000024.10:18991722:T:C	NC_000024.10:18991722:T:C	(self)
ss10580816, ss12058302	NT_011875.9:7240965:T:C	NC_000024.10:18991722:T:C	(self)
ss14801451, ss18052487, ss19825364	NT_011875.10:7240943:T:C	NC_000024.10:18991722:T:C	(self)
ss22884070, ss43980591, ss105778606, ss133743876, ss144449620, ss157863181, ss169061376	NT_011875.12:7355030:T:C	NC_000024.10:18991722:T:C	(self)
ss5666143608	NC_000024.9:21153608:T:G	NC_000024.10:18991722:T:G

Publications tab displays PubMed articles citing the variation as a listing of PMID, Title, Author, Year, Journal, ordered by Year, descending.

No publications for rs6530602

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

rs6530602