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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.

rs16648

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chrY:12925843-12925845 (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
delGA / dupGA
Variation Type
Indel Insertion and Deletion
Frequency
delGA=0.02534 (782/30855, GnomAD)
AGA=0.00 (0/20, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
None
Publications
1 citation
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.12925844_12925845del
GRCh38.p13 chr Y NC_000024.10:g.12925844_12925845dup
GRCh37.p13 chr Y NC_000024.9:g.15037755_15037756insGA
GRCh37.p13 chr Y NC_000024.9:g.15037755_15037756insGAGA
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
gnomAD - Genomes Global Study-wide 30855 AGA=0.97466 delGA=0.02534
gnomAD - Genomes European Sub 16646 AGA=0.97339 delGA=0.02661
gnomAD - Genomes African Sub 8728 AGA=0.9943 delGA=0.0057
gnomAD - Genomes American Sub 3448 AGA=0.9382 delGA=0.0618
gnomAD - Genomes East Asian Sub 781 AGA=1.000 delGA=0.000
gnomAD - Genomes Ashkenazi Jewish Sub 760 AGA=0.921 delGA=0.079
gnomAD - Genomes Other Sub 492 AGA=0.967 delGA=0.033
The Danish reference pan genome Danish Study-wide 20 -

No frequency provided

dupGA=1.00
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 AGA= delGA dupGA
GRCh38.p13 chr Y NC_000024.10:g.12925843_12925845= NC_000024.10:g.12925844_12925845del NC_000024.10:g.12925844_12925845dup
GRCh37.p13 chr Y NC_000024.9:g.15037755_15037756insGA NC_000024.9:g.15037755= NC_000024.9:g.15037755_15037756insGAGA
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#.

19 SubSNP, 2 Frequency submissions
No Submitter Submission ID Date (Build)
1 MARSHFIELD ss19053 Sep 19, 2000 (60)
2 ABI ss43751017 Mar 14, 2006 (126)
3 GMI ss155886573 Dec 01, 2009 (131)
4 BUSHMAN ss194074604 Jul 04, 2010 (132)
5 BL ss256210339 May 09, 2011 (135)
6 GMI ss288570996 May 09, 2011 (134)
7 GMI ss478865953 May 04, 2012 (137)
8 TISHKOFF ss567118724 Apr 25, 2013 (138)
9 SSMP ss664588561 Apr 09, 2015 (144)
10 BILGI_BIOE ss666792550 Apr 25, 2013 (138)
11 DDI ss1536954313 Apr 09, 2015 (144)
12 EVA_GENOME_DK ss1577677070 Apr 09, 2015 (144)
13 SYSTEMSBIOZJU ss2629804633 Oct 12, 2018 (152)
14 SWEGEN ss3020947415 Oct 12, 2018 (152)
15 PACBIO ss3788975728 Jul 14, 2019 (153)
16 PACBIO ss3793846093 Jul 14, 2019 (153)
17 PACBIO ss3798730587 Jul 14, 2019 (153)
18 EVA ss3836373297 Apr 27, 2020 (154)
19 GNOMAD ss4126128524 Apr 27, 2021 (155)
20 The Danish reference pan genome NC_000024.9 - 15037755 Apr 27, 2020 (154)
21 gnomAD - Genomes NC_000024.10 - 12925843 Apr 27, 2021 (155)
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).

Associated ID History Updated (Build)
rs140230625 Sep 17, 2011 (135)
rs144550173 Sep 17, 2011 (135)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
594962390, ss4126128524 NC_000024.10:12925842:AG: NC_000024.10:12925842:AGA:A
ss256210339, ss478865953 NC_000024.8:13547148::AG NC_000024.10:12925842:AGA:AGAGA (self)
1356802, ss664588561, ss666792550, ss1536954313, ss1577677070, ss2629804633, ss3020947415, ss3788975728, ss3793846093, ss3798730587, ss3836373297 NC_000024.9:15037754::AG NC_000024.10:12925842:AGA:AGAGA (self)
ss567118724 NC_000024.9:15037755::GA NC_000024.10:12925842:AGA:AGAGA (self)
ss19053, ss43751017, ss194074604, ss288570996 NT_011875.12:1239176::AG NC_000024.10:12925842:AGA:AGAGA (self)
ss155886573 NT_011875.12:1239177::GA NC_000024.10:12925842:AGA:AGAGA (self)
Help

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

1 citation for rs16648
PMID Title Author Year Journal
19495413 Improved resolution haplogroup G phylogeny in the Y chromosome, revealed by a set of newly characterized SNPs. Sims LM et al. 2009 PloS one
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