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dbSNP Short Genetic Variations

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.

rs4932620

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr15:28269135 (GRCh38.p12) 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>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.02435 (3058/125568, TOPMED)
T=0.0204 (640/31408, GnomAD)
T=0.063 (317/5008, 1000G) (+ 4 more)
T=0.001 (6/4480, Estonian)
T=0.004 (17/3854, ALSPAC)
T=0.006 (22/3708, TWINSUK)
T=0.00 (0/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HERC2 : Intron Variant
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.p12 chr 15 NC_000015.10:g.28269135T>A
GRCh38.p12 chr 15 NC_000015.10:g.28269135T>C
GRCh37.p13 chr 15 NC_000015.9:g.28514281T>A
GRCh37.p13 chr 15 NC_000015.9:g.28514281T>C
HERC2 RefSeqGene NG_016355.1:g.58015A>T
HERC2 RefSeqGene NG_016355.1:g.58015A>G
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.402580C>T
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.402580C>A
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.516366C>T
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.516366C>A
Gene: HERC2, HECT and RLD domain containing E3 ubiquitin protein ligase 2 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
HERC2 transcript NM_004667.5:c. N/A Intron Variant
HERC2 transcript variant X3 XM_005268276.5:c. N/A Intron Variant
HERC2 transcript variant X1 XM_006720726.3:c. N/A Intron Variant
HERC2 transcript variant X5 XM_006720727.3:c. N/A Intron Variant
HERC2 transcript variant X2 XM_017022695.1:c. N/A Intron Variant
HERC2 transcript variant X4 XM_017022696.1:c. N/A Intron Variant
HERC2 transcript variant X8 XM_017022697.1:c. N/A Genic Upstream Transcript Variant
HERC2 transcript variant X9 XM_017022698.1:c. N/A Genic Upstream Transcript Variant
HERC2 transcript variant X7 XR_001751410.1:n. N/A Intron Variant
HERC2 transcript variant X6 XR_931930.2:n. N/A Intron Variant
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
TopMed Global Study-wide 125568 T=0.02435 C=0.97565
gnomAD - Genomes Global Study-wide 31408 T=0.0204 C=0.9796
gnomAD - Genomes European Sub 18912 T=0.0034 C=0.9966
gnomAD - Genomes African Sub 8710 T=0.059 C=0.941
gnomAD - Genomes East Asian Sub 1560 T=0.011 C=0.989
gnomAD - Genomes Other Sub 1088 T=0.016 C=0.984
gnomAD - Genomes American Sub 848 T=0.01 C=0.99
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.04 C=0.96
1000Genomes Global Study-wide 5008 T=0.063 C=0.937
1000Genomes African Sub 1322 T=0.085 C=0.915
1000Genomes East Asian Sub 1008 T=0.017 C=0.983
1000Genomes Europe Sub 1006 T=0.016 C=0.984
1000Genomes South Asian Sub 978 T=0.16 C=0.84
1000Genomes American Sub 694 T=0.01 C=0.99
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.001 C=0.999
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.004 C=0.996
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.006 C=0.994
Northern Sweden ACPOP Study-wide 600 T=0.00 C=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 T= A C Note
GRCh38.p12 chr 15 NC_000015.10:g.28...

NC_000015.10:g.28269135=

NC_000015.10:g.28...

NC_000015.10:g.28269135T>A

NC_000015.10:g.28...

NC_000015.10:g.28269135T>C

GRCh37.p13 chr 15 NC_000015.9:g.285...

NC_000015.9:g.28514281=

NC_000015.9:g.285...

NC_000015.9:g.28514281T>A

NC_000015.9:g.285...

NC_000015.9:g.28514281T>C

HERC2 RefSeqGene NG_016355.1:g.58015= NG_016355.1:g.580...

NG_016355.1:g.58015A>T

NG_016355.1:g.580...

NG_016355.1:g.58015A>G

chr 15 fix patch HG2139_PATCH NW_011332701.1:g....

NW_011332701.1:g.402580C>T

NW_011332701.1:g....

NW_011332701.1:g.402580C>A

NW_011332701.1:g....

NW_011332701.1:g.402580=

GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.516...

NT_187660.1:g.516366C>T

NT_187660.1:g.516...

NT_187660.1:g.516366C>A

NT_187660.1:g.516...

NT_187660.1:g.516366=

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#.

73 SubSNP, 7 Frequency submissions
No Submitter Submission ID Date (Build)
1 WI_SSAHASNP ss6820956 Feb 20, 2003 (111)
2 BCM_SSAHASNP ss10799148 Jul 11, 2003 (116)
3 SSAHASNP ss21271787 Apr 05, 2004 (121)
4 AFFY ss66501641 Nov 29, 2006 (127)
5 AFFY ss76324606 Dec 08, 2007 (130)
6 HGSV ss80526560 Dec 15, 2007 (130)
7 KRIBB_YJKIM ss82166807 Dec 14, 2007 (130)
8 HGSV ss84014105 Dec 15, 2007 (130)
9 HGSV ss84881576 Dec 15, 2007 (130)
10 BCMHGSC_JDW ss90104100 Mar 24, 2008 (129)
11 HUMANGENOME_JCVI ss96746397 Feb 05, 2009 (130)
12 BGI ss106418986 Feb 05, 2009 (130)
13 1000GENOMES ss108696681 Jan 23, 2009 (130)
14 ILLUMINA-UK ss118172298 Feb 14, 2009 (130)
15 ENSEMBL ss134210705 Dec 01, 2009 (131)
16 ENSEMBL ss136931698 Dec 01, 2009 (131)
17 GMI ss156361612 Dec 01, 2009 (131)
18 ILLUMINA ss161050651 Dec 01, 2009 (131)
19 COMPLETE_GENOMICS ss167717302 Jul 04, 2010 (132)
20 COMPLETE_GENOMICS ss170885053 Jul 04, 2010 (132)
21 BCM-HGSC-SUB ss207182181 Jul 04, 2010 (132)
22 1000GENOMES ss211585715 Jul 14, 2010 (132)
23 1000GENOMES ss226813714 Jul 14, 2010 (132)
24 1000GENOMES ss236722881 Jul 15, 2010 (132)
25 1000GENOMES ss243120803 Jul 15, 2010 (132)
26 BL ss254862602 May 09, 2011 (134)
27 GMI ss282193278 May 04, 2012 (137)
28 GMI ss286924801 Apr 25, 2013 (138)
29 PJP ss291808414 May 09, 2011 (134)
30 ILLUMINA ss479438248 Sep 08, 2015 (146)
31 ILLUMINA ss537295107 Sep 08, 2015 (146)
32 TISHKOFF ss564384304 Apr 25, 2013 (138)
33 SSMP ss660096423 Apr 25, 2013 (138)
34 ILLUMINA ss778706872 Sep 08, 2015 (146)
35 ILLUMINA ss834165954 Sep 08, 2015 (146)
36 JMKIDD_LAB ss1080004195 Aug 21, 2014 (142)
37 1000GENOMES ss1352827234 Aug 21, 2014 (142)
38 DDI ss1427576145 Apr 01, 2015 (144)
39 EVA_GENOME_DK ss1577523244 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1632673346 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1675667379 Apr 01, 2015 (144)
42 EVA_DECODE ss1695637160 Apr 01, 2015 (144)
43 EVA_MGP ss1711390277 Apr 01, 2015 (144)
44 EVA_SVP ss1713477717 Apr 01, 2015 (144)
45 WEILL_CORNELL_DGM ss1935022920 Feb 12, 2016 (147)
46 GENOMED ss1968070895 Jul 19, 2016 (147)
47 JJLAB ss2028291437 Sep 14, 2016 (149)
48 USC_VALOUEV ss2156688501 Dec 20, 2016 (150)
49 HUMAN_LONGEVITY ss2205535025 Dec 20, 2016 (150)
50 TOPMED ss2370076784 Dec 20, 2016 (150)
51 SYSTEMSBIOZJU ss2628638982 Nov 08, 2017 (151)
52 ILLUMINA ss2633208818 Nov 08, 2017 (151)
53 GRF ss2701147735 Nov 08, 2017 (151)
54 GNOMAD ss2933004436 Nov 08, 2017 (151)
55 SWEGEN ss3013008120 Nov 08, 2017 (151)
56 BIOINF_KMB_FNS_UNIBA ss3027969928 Nov 08, 2017 (151)
57 TOPMED ss3223273083 Nov 08, 2017 (151)
58 TOPMED ss3223273084 Nov 08, 2017 (151)
59 CSHL ss3351042301 Nov 08, 2017 (151)
60 ILLUMINA ss3627323642 Oct 12, 2018 (152)
61 ILLUMINA ss3631203133 Oct 12, 2018 (152)
62 ILLUMINA ss3636288491 Oct 12, 2018 (152)
63 ILLUMINA ss3641057896 Oct 12, 2018 (152)
64 ILLUMINA ss3641353159 Oct 12, 2018 (152)
65 URBANLAB ss3650317315 Oct 12, 2018 (152)
66 EGCUT_WGS ss3680178698 Jul 13, 2019 (153)
67 EVA_DECODE ss3697586804 Jul 13, 2019 (153)
68 ACPOP ss3740788037 Jul 13, 2019 (153)
69 EVA ss3752892852 Jul 13, 2019 (153)
70 PACBIO ss3787801306 Jul 13, 2019 (153)
71 PACBIO ss3792820479 Jul 13, 2019 (153)
72 PACBIO ss3797704942 Jul 13, 2019 (153)
73 KHV_HUMAN_GENOMES ss3818209970 Jul 13, 2019 (153)
74 1000Genomes NC_000015.9 - 28514281 Oct 12, 2018 (152)
75 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 28514281 Oct 12, 2018 (152)
76 Genetic variation in the Estonian population NC_000015.9 - 28514281 Oct 12, 2018 (152)
77 gnomAD - Genomes NC_000015.9 - 28514281 Jul 13, 2019 (153)
78 Northern Sweden NC_000015.9 - 28514281 Jul 13, 2019 (153)
79 TopMed NC_000015.10 - 28269135 Oct 12, 2018 (152)
80 UK 10K study - Twins NC_000015.9 - 28514281 Oct 12, 2018 (152)
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)
rs56615886 May 25, 2008 (130)
rs57342079 Feb 26, 2009 (130)
rs59142487 May 25, 2008 (130)
Added to this RefSNP Cluster:
Submission ids Observation SPDI Canonical SPDI Source RSIDs
ss3223273083 NC_000015.10:28269134:T:A NC_000015.10:28269134:T:A (self)
ss80526560, ss84014105, ss84881576, ss90104100, ss108696681, ss118172298, ss167717302, ss170885053, ss207182181, ss211585715, ss254862602, ss282193278, ss286924801, ss291808414, ss1695637160, ss1713477717 NC_000015.8:26187875:T:C NC_000015.10:28269134:T:C (self)
65874594, 36577663, 25916946, 179711917, 14072902, 36577663, ss226813714, ss236722881, ss243120803, ss479438248, ss537295107, ss564384304, ss660096423, ss778706872, ss834165954, ss1080004195, ss1352827234, ss1427576145, ss1577523244, ss1632673346, ss1675667379, ss1711390277, ss1935022920, ss1968070895, ss2028291437, ss2156688501, ss2370076784, ss2628638982, ss2633208818, ss2701147735, ss2933004436, ss3013008120, ss3351042301, ss3627323642, ss3631203133, ss3636288491, ss3641057896, ss3641353159, ss3680178698, ss3740788037, ss3752892852, ss3787801306, ss3792820479, ss3797704942 NC_000015.9:28514280:T:C NC_000015.10:28269134:T:C (self)
125955010, ss2205535025, ss3027969928, ss3223273084, ss3650317315, ss3697586804, ss3818209970 NC_000015.10:28269134:T:C NC_000015.10:28269134:T:C (self)
ss10799148 NT_010280.15:873538:T:C NC_000015.10:28269134:T:C (self)
ss21271787 NT_010280.16:879771:T:C NC_000015.10:28269134:T:C (self)
ss6820956, ss66501641, ss76324606, ss82166807, ss96746397, ss106418986, ss134210705, ss136931698, ss156361612, ss161050651 NT_026446.14:4949427:T:C NC_000015.10:28269134:T:C (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 rs4932620

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.post104+4a6ee9c