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dbSNP Short Genetic Variations

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.

rs17249974

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrY:17155464 (GRCh38.p13) 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
A>C / A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.0057 (8/1398, KOREAN)
A=0.2660 (328/1233, 1000G)
A=0.388 (348/896, chrY) (+ 5 more)
A=0.000 (0/298, SGDP_PRJ)
A=0.09 (5/53, Qatari)
A=0.25 (6/24, Ancient Sardinia)
A=0.00 (0/24, Siberian)
A=0.30 (6/20, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
0 citations
Genomic View
See rs on genome
Help

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.p13 chr Y NC_000024.10:g.17155464A>C
GRCh38.p13 chr Y NC_000024.10:g.17155464A>G
GRCh38.p13 chr Y NC_000024.10:g.17155464A>T
GRCh37.p13 chr Y NC_000024.9:g.19267344A>C
GRCh37.p13 chr Y NC_000024.9:g.19267344A>G
GRCh37.p13 chr Y NC_000024.9:g.19267344A>T
Help

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
Help

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
KOREAN population from KRGDB KOREAN Study-wide 1398 A=0.0057 C=0.9943, G=0.0000, T=0.0000
1000Genomes Global Study-wide 1233 A=0.2660 C=0.7340
1000Genomes African Sub 319 A=0.038 C=0.962
1000Genomes South Asian Sub 260 A=0.388 C=0.612
1000Genomes East Asian Sub 244 A=0.004 C=0.996
1000Genomes Europe Sub 240 A=0.583 C=0.417
1000Genomes American Sub 170 A=0.435 C=0.565
chrY_custom_capture Global Study-wide 896 A=0.388 C=0.612
chrY_custom_capture AFP Sub 0 A=0 C=0
chrY_custom_capture AHG Sub 0 A=0 C=0
chrY_custom_capture ASC Sub 0 A=0 C=0
chrY_custom_capture ASE Sub 0 A=0 C=0
chrY_custom_capture AUS Sub 0 A=0 C=0
chrY_custom_capture BRI Sub 0 A=0 C=0
chrY_custom_capture ENV Sub 0 A=0 C=0
chrY_custom_capture ESC Sub 0 A=0 C=0
chrY_custom_capture ESE Sub 0 A=0 C=0
chrY_custom_capture ESW Sub 0 A=0 C=0
chrY_custom_capture MEX Sub 0 A=0 C=0
chrY_custom_capture MNE Sub 0 A=0 C=0
chrY_custom_capture SCA Sub 0 A=0 C=0
SGDP_PRJ Global Study-wide 298 A=0.000 C=1.000
Qatari Global Study-wide 53 A=0.09 C=0.91
Ancient Sardinia genome-wide 1240k capture data generation and analysis Global Study-wide 24 A=0.25 C=0.75
Siberian Global Study-wide 24 A=0.00 C=1.00
The Danish reference pan genome Danish Study-wide 20 A=0.30 C=0.70
Help

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 A= C G T
GRCh38.p13 chr Y NC_000024.10:g.17155464= NC_000024.10:g.17155464A>C NC_000024.10:g.17155464A>G NC_000024.10:g.17155464A>T
GRCh37.p13 chr Y NC_000024.9:g.19267344= NC_000024.9:g.19267344A>C NC_000024.9:g.19267344A>G NC_000024.9:g.19267344A>T
Help

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#.

38 SubSNP, 8 Frequency submissions
No Submitter Submission ID Date (Build)
1 PERLEGEN ss24726322 Sep 20, 2004 (123)
2 BGI ss105778541 Feb 04, 2009 (130)
3 ILLUMINA-UK ss115582168 Feb 04, 2009 (130)
4 GMI ss157862379 Dec 01, 2009 (131)
5 COMPLETE_GENOMICS ss162983654 Jul 04, 2010 (132)
6 BUSHMAN ss204418889 Jul 04, 2010 (132)
7 GMI ss283923596 May 04, 2012 (137)
8 TISHKOFF ss567115781 Apr 25, 2013 (138)
9 SSMP ss663099477 Apr 25, 2013 (138)
10 HUMGEN ss778079549 Aug 21, 2014 (142)
11 JOBLING_UOL ss1399963444 Apr 01, 2015 (144)
12 DDI ss1432160803 Apr 01, 2015 (144)
13 1000GENOMES ss1556771808 Apr 01, 2015 (144)
14 EVA_GENOME_DK ss1583556455 Apr 01, 2015 (144)
15 WEILL_CORNELL_DGM ss1939863602 Feb 12, 2016 (147)
16 ILLUMINA ss1958179341 Feb 12, 2016 (147)
17 ILLUMINA ss1958179342 Feb 12, 2016 (147)
18 USC_VALOUEV ss2159356337 Dec 20, 2016 (150)
19 HUMAN_LONGEVITY ss2321458982 Dec 20, 2016 (150)
20 SYSTEMSBIOZJU ss2629805364 Nov 08, 2017 (151)
21 GRF ss2710440745 Nov 08, 2017 (151)
22 SWEGEN ss3020958625 Nov 08, 2017 (151)
23 ILLUMINA ss3023054520 Nov 08, 2017 (151)
24 ILLUMINA ss3023054521 Nov 08, 2017 (151)
25 HUMGEN ss3029950915 Nov 08, 2017 (151)
26 ILLUMINA ss3641266425 Oct 12, 2018 (152)
27 ILLUMINA ss3641565388 Oct 12, 2018 (152)
28 ILLUMINA ss3653613108 Oct 12, 2018 (152)
29 ILLUMINA ss3653613109 Oct 12, 2018 (152)
30 PACBIO ss3788976628 Jul 14, 2019 (153)
31 PACBIO ss3793847142 Jul 14, 2019 (153)
32 PACBIO ss3798731620 Jul 14, 2019 (153)
33 KHV_HUMAN_GENOMES ss3823538447 Jul 14, 2019 (153)
34 EVA ss3836374859 Apr 27, 2020 (154)
35 SGDP_PRJ ss3892740022 Apr 27, 2020 (154)
36 KRGDB ss3943528772 Apr 27, 2020 (154)
37 EVA ss3984772877 Apr 27, 2021 (155)
38 EVA ss3985998844 Apr 27, 2021 (155)
39 1000Genomes NC_000024.9 - 19267344 Oct 12, 2018 (152)
40 chrY_custom_capture NC_000024.9 - 19267344 Apr 27, 2020 (154)
41 The Danish reference pan genome NC_000024.9 - 19267344 Apr 27, 2020 (154)
42 KOREAN population from KRGDB NC_000024.9 - 19267344 Apr 27, 2020 (154)
43 Ancient Sardinia genome-wide 1240k capture data generation and analysis NC_000024.9 - 19267344 Apr 27, 2021 (155)
44 Qatari NC_000024.9 - 19267344 Apr 27, 2020 (154)
45 SGDP_PRJ NC_000024.9 - 19267344 Apr 27, 2020 (154)
46 Siberian NC_000024.9 - 19267344 Apr 27, 2020 (154)
Help

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
ss162983654, ss204418889, ss283923596 NC_000024.8:17776737:A:C NC_000024.10:17155463:A:C (self)
84724796, 10707, 9721392, 50706166, 1224771, 21905524, 44757002, 11872691, ss567115781, ss663099477, ss778079549, ss1399963444, ss1432160803, ss1556771808, ss1583556455, ss1939863602, ss1958179341, ss1958179342, ss2159356337, ss2629805364, ss2710440745, ss3020958625, ss3023054520, ss3023054521, ss3029950915, ss3641266425, ss3641565388, ss3653613108, ss3653613109, ss3788976628, ss3793847142, ss3798731620, ss3836374859, ss3892740022, ss3943528772, ss3984772877, ss3985998844 NC_000024.9:19267343:A:C NC_000024.10:17155463:A:C (self)
ss2321458982, ss3823538447 NC_000024.10:17155463:A:C NC_000024.10:17155463:A:C (self)
ss24726322, ss105778541, ss115582168, ss157862379 NT_011875.12:5468765:A:C NC_000024.10:17155463:A:C (self)
50706166, ss3943528772 NC_000024.9:19267343:A:G NC_000024.10:17155463:A:G (self)
50706166, ss3943528772 NC_000024.9:19267343:A:T NC_000024.10:17155463:A:T (self)
Help

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

No publications for rs17249974

Help

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.

Software version is: 2.0.1.post596+ae089ad