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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.

rs6497271

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr15:28120285 (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
A>C / A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.16550 (20781/125568, TOPMED)
A=0.1490 (4676/31378, GnomAD)
A=0.212 (1061/5008, 1000G) (+ 3 more)
A=0.001 (6/4480, Estonian)
A=0.00 (0/600, NorthernSweden)
A=0.02 (4/212, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
HERC2 : Intron Variant
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.p12 chr 15 NC_000015.10:g.28120285A>C
GRCh38.p12 chr 15 NC_000015.10:g.28120285A>G
GRCh37.p13 chr 15 NC_000015.9:g.28365431A>C
GRCh37.p13 chr 15 NC_000015.9:g.28365431A>G
HERC2 RefSeqGene NG_016355.1:g.206865T>G
HERC2 RefSeqGene NG_016355.1:g.206865T>C
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.253724G>A
chr 15 fix patch HG2139_PATCH NW_011332701.1:g.253724G>C
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.253724G>A
GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.253724G>C
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 Intron Variant
HERC2 transcript variant X9 XM_017022698.1:c. N/A Intron Variant
HERC2 transcript variant X7 XR_001751410.1:n. N/A Genic Downstream Transcript Variant
HERC2 transcript variant X6 XR_931930.2:n. N/A Genic Downstream Transcript 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 A=0.16550 G=0.83450
gnomAD - Genomes Global Study-wide 31378 A=0.1490 G=0.8510
gnomAD - Genomes European Sub 18908 A=0.0040 G=0.9960
gnomAD - Genomes African Sub 8686 A=0.514 G=0.486
gnomAD - Genomes East Asian Sub 1560 A=0.022 G=0.978
gnomAD - Genomes Other Sub 1088 A=0.045 G=0.955
gnomAD - Genomes American Sub 846 A=0.04 G=0.96
gnomAD - Genomes Ashkenazi Jewish Sub 290 A=0.04 G=0.96
1000Genomes Global Study-wide 5008 A=0.212 G=0.788
1000Genomes African Sub 1322 A=0.626 G=0.374
1000Genomes East Asian Sub 1008 A=0.021 G=0.979
1000Genomes Europe Sub 1006 A=0.016 G=0.984
1000Genomes South Asian Sub 978 A=0.16 G=0.84
1000Genomes American Sub 694 A=0.05 G=0.95
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.001 G=0.999
Northern Sweden ACPOP Study-wide 600 A=0.00 G=1.00
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.02 G=0.98
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 Note
GRCh38.p12 chr 15 NC_000015.10:g.28...

NC_000015.10:g.28120285=

NC_000015.10:g.28...

NC_000015.10:g.28120285A>C

NC_000015.10:g.28...

NC_000015.10:g.28120285A>G

GRCh37.p13 chr 15 NC_000015.9:g.283...

NC_000015.9:g.28365431=

NC_000015.9:g.283...

NC_000015.9:g.28365431A>C

NC_000015.9:g.283...

NC_000015.9:g.28365431A>G

HERC2 RefSeqGene NG_016355.1:g.206...

NG_016355.1:g.206865=

NG_016355.1:g.206...

NG_016355.1:g.206865T>G

NG_016355.1:g.206...

NG_016355.1:g.206865T>C

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

NW_011332701.1:g.253724G>A

NW_011332701.1:g....

NW_011332701.1:g.253724G>C

NW_011332701.1:g....

NW_011332701.1:g.253724=

GRCh38.p12 chr 15 alt locus HSCHR15_4_CTG8 NT_187660.1:g.253...

NT_187660.1:g.253724G>A

NT_187660.1:g.253...

NT_187660.1:g.253724G>C

NT_187660.1:g.253...

NT_187660.1:g.253724=

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#.

74 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 BCM_SSAHASNP ss10777322 Jul 11, 2003 (116)
2 WI_SSAHASNP ss12321574 Jul 11, 2003 (116)
3 SSAHASNP ss21271079 Apr 05, 2004 (121)
4 ILLUMINA ss75209527 Dec 06, 2007 (129)
5 HGSV ss77509717 Dec 06, 2007 (129)
6 BCMHGSC_JDW ss90103965 Mar 24, 2008 (129)
7 HUMANGENOME_JCVI ss96746333 Feb 05, 2009 (130)
8 BGI ss106418948 Feb 05, 2009 (130)
9 1000GENOMES ss108696411 Jan 23, 2009 (130)
10 KRIBB_YJKIM ss119512720 Dec 01, 2009 (131)
11 ENSEMBL ss134210386 Dec 01, 2009 (131)
12 ENSEMBL ss136931806 Dec 01, 2009 (131)
13 GMI ss156360719 Dec 01, 2009 (131)
14 ILLUMINA ss161050451 Dec 01, 2009 (131)
15 COMPLETE_GENOMICS ss167716473 Jul 04, 2010 (132)
16 COMPLETE_GENOMICS ss170884593 Jul 04, 2010 (132)
17 ILLUMINA ss174018410 Jul 04, 2010 (132)
18 BUSHMAN ss200654652 Jul 04, 2010 (132)
19 BCM-HGSC-SUB ss207207446 Jul 04, 2010 (132)
20 1000GENOMES ss211585659 Jul 14, 2010 (132)
21 1000GENOMES ss226813402 Jul 14, 2010 (132)
22 1000GENOMES ss236722744 Jul 15, 2010 (132)
23 1000GENOMES ss243120676 Jul 15, 2010 (132)
24 BL ss254862252 May 09, 2011 (134)
25 GMI ss282193024 May 04, 2012 (137)
26 GMI ss286924733 Apr 25, 2013 (138)
27 PJP ss291808327 May 09, 2011 (134)
28 ILLUMINA ss479418728 Sep 08, 2015 (146)
29 ILLUMINA ss483376278 May 04, 2012 (137)
30 ILLUMINA ss483626860 May 04, 2012 (137)
31 ILLUMINA ss535830739 Sep 08, 2015 (146)
32 TISHKOFF ss564383852 Apr 25, 2013 (138)
33 ILLUMINA ss782256781 Aug 21, 2014 (142)
34 ILLUMINA ss835836033 Aug 21, 2014 (142)
35 JMKIDD_LAB ss1080003579 Aug 21, 2014 (142)
36 1000GENOMES ss1352822765 Aug 21, 2014 (142)
37 DDI ss1427575981 Apr 01, 2015 (144)
38 EVA_GENOME_DK ss1577523103 Apr 01, 2015 (144)
39 EVA_UK10K_ALSPAC ss1632671820 Apr 01, 2015 (144)
40 EVA_UK10K_ALSPAC ss1632671821 Apr 01, 2015 (144)
41 EVA_UK10K_TWINSUK ss1675665853 Apr 01, 2015 (144)
42 EVA_UK10K_TWINSUK ss1675665854 Apr 01, 2015 (144)
43 EVA_DECODE ss1695636280 Apr 01, 2015 (144)
44 EVA_SVP ss1713477661 Apr 01, 2015 (144)
45 HAMMER_LAB ss1808131529 Sep 08, 2015 (146)
46 WEILL_CORNELL_DGM ss1935021785 Feb 12, 2016 (147)
47 GENOMED ss1968070799 Jul 19, 2016 (147)
48 JJLAB ss2028291162 Sep 14, 2016 (149)
49 USC_VALOUEV ss2156688197 Dec 20, 2016 (150)
50 HUMAN_LONGEVITY ss2205531708 Dec 20, 2016 (150)
51 TOPMED ss2370067384 Dec 20, 2016 (150)
52 SYSTEMSBIOZJU ss2628638809 Nov 08, 2017 (151)
53 ILLUMINA ss2633208763 Nov 08, 2017 (151)
54 GRF ss2701147208 Nov 08, 2017 (151)
55 GNOMAD ss2932991532 Nov 08, 2017 (151)
56 SWEGEN ss3013006616 Nov 08, 2017 (151)
57 BIOINF_KMB_FNS_UNIBA ss3027969855 Nov 08, 2017 (151)
58 TOPMED ss3223244381 Nov 08, 2017 (151)
59 CSHL ss3351042101 Nov 08, 2017 (151)
60 ILLUMINA ss3627323442 Oct 12, 2018 (152)
61 ILLUMINA ss3631203082 Oct 12, 2018 (152)
62 ILLUMINA ss3636288276 Oct 12, 2018 (152)
63 ILLUMINA ss3638075922 Oct 12, 2018 (152)
64 ILLUMINA ss3641904527 Oct 12, 2018 (152)
65 ILLUMINA ss3643060629 Oct 12, 2018 (152)
66 URBANLAB ss3650317226 Oct 12, 2018 (152)
67 EGCUT_WGS ss3680178182 Jul 13, 2019 (153)
68 EVA_DECODE ss3697585256 Jul 13, 2019 (153)
69 ACPOP ss3740787486 Jul 13, 2019 (153)
70 EVA ss3752891784 Jul 13, 2019 (153)
71 PACBIO ss3787801168 Jul 13, 2019 (153)
72 PACBIO ss3792820395 Jul 13, 2019 (153)
73 PACBIO ss3797704856 Jul 13, 2019 (153)
74 KHV_HUMAN_GENOMES ss3818208950 Jul 13, 2019 (153)
75 1000Genomes NC_000015.9 - 28365431 Oct 12, 2018 (152)
76 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 36575985 (NC_000015.9:28365430:A:A 19/3854, NC_000015.9:28365430:A:G 3835/3854)
Row 36575986 (NC_000015.9:28365430:A:A 3854/3854, NC_000015.9:28365430:A:C 0/3854)

- Oct 12, 2018 (152)
77 The Avon Longitudinal Study of Parents and Children

Submission ignored due to conflicting rows:
Row 36575985 (NC_000015.9:28365430:A:A 19/3854, NC_000015.9:28365430:A:G 3835/3854)
Row 36575986 (NC_000015.9:28365430:A:A 3854/3854, NC_000015.9:28365430:A:C 0/3854)

- Oct 12, 2018 (152)
78 Genetic variation in the Estonian population NC_000015.9 - 28365431 Oct 12, 2018 (152)
79 gnomAD - Genomes NC_000015.9 - 28365431 Jul 13, 2019 (153)
80 Northern Sweden NC_000015.9 - 28365431 Jul 13, 2019 (153)
81 TopMed NC_000015.10 - 28120285 Oct 12, 2018 (152)
82 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 36575985 (NC_000015.9:28365430:A:A 25/3708, NC_000015.9:28365430:A:G 3683/3708)
Row 36575986 (NC_000015.9:28365430:A:A 3707/3708, NC_000015.9:28365430:A:C 1/3708)

- Oct 12, 2018 (152)
83 UK 10K study - Twins

Submission ignored due to conflicting rows:
Row 36575985 (NC_000015.9:28365430:A:A 25/3708, NC_000015.9:28365430:A:G 3683/3708)
Row 36575986 (NC_000015.9:28365430:A:A 3707/3708, NC_000015.9:28365430:A:C 1/3708)

- Oct 12, 2018 (152)
84 A Vietnamese Genetic Variation Database NC_000015.9 - 28365431 Jul 13, 2019 (153)
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
ss1632671821, ss1675665854 NC_000015.9:28365430:A:C NC_000015.10:28120284:A:C (self)
ss2205531708 NC_000015.10:28120284:A:C NC_000015.10:28120284:A:C (self)
ss77509717, ss90103965, ss108696411, ss167716473, ss170884593, ss200654652, ss207207446, ss211585659, ss254862252, ss282193024, ss286924733, ss291808327, ss483376278, ss1695636280, ss1713477661, ss3643060629 NC_000015.8:26039025:A:G NC_000015.10:28120284:A:G (self)
65869985, 25916430, 179699635, 14072351, 8138100, ss226813402, ss236722744, ss243120676, ss479418728, ss483626860, ss535830739, ss564383852, ss782256781, ss835836033, ss1080003579, ss1352822765, ss1427575981, ss1577523103, ss1632671820, ss1675665853, ss1808131529, ss1935021785, ss1968070799, ss2028291162, ss2156688197, ss2370067384, ss2628638809, ss2633208763, ss2701147208, ss2932991532, ss3013006616, ss3351042101, ss3627323442, ss3631203082, ss3636288276, ss3638075922, ss3641904527, ss3680178182, ss3740787486, ss3752891784, ss3787801168, ss3792820395, ss3797704856 NC_000015.9:28365430:A:G NC_000015.10:28120284:A:G (self)
125931496, ss2205531708, ss3027969855, ss3223244381, ss3650317226, ss3697585256, ss3818208950 NC_000015.10:28120284:A:G NC_000015.10:28120284:A:G (self)
ss10777322, ss12321574 NT_010280.15:724688:A:G NC_000015.10:28120284:A:G (self)
ss21271079 NT_010280.16:730921:A:G NC_000015.10:28120284:A:G (self)
ss75209527, ss96746333, ss106418948, ss119512720, ss134210386, ss136931806, ss156360719, ss161050451, ss174018410 NT_026446.14:4800577:A:G NC_000015.10:28120284:A:G (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 rs6497271
PMID Title Author Year Journal
18252222 A single SNP in an evolutionary conserved region within intron 86 of the HERC2 gene determines human blue-brown eye color. Sturm RA et al. 2008 American journal of human genetics

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