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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs4446909

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chrY:1614890 (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.

This SNP has mapping conflicts. See here for details.

Alleles
G>A / G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.180589 (47800/264690, TOPMED)
A=0.175196 (24506/139878, GnomAD)
A=0.22472 (10401/46284, ALFA) (+ 9 more)
A=0.28764 (8128/28258, 14KJPN)
A=0.28783 (4824/16760, 8.3KJPN)
A=0.1702 (818/4805, 1000G_30x)
A=0.1743 (658/3775, 1000G)
A=0.192 (63/328, HapMap)
G=0.428 (71/166, SGDP_PRJ)
A=0.148 (16/108, Qatari)
A=0.28 (11/40, GENOME_DK)
A=0.10 (3/30, Vietnamese)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
ASMT : Intron Variant
Publications
6 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 46284 G=0.77528 A=0.22472, T=0.00000
European Sub 36050 G=0.75207 A=0.24793, T=0.00000
African Sub 5154 G=0.9530 A=0.0470, T=0.0000
African Others Sub 156 G=0.994 A=0.006, T=0.000
African American Sub 4998 G=0.9518 A=0.0482, T=0.0000
Asian Sub 468 G=0.707 A=0.293, T=0.000
East Asian Sub 404 G=0.703 A=0.297, T=0.000
Other Asian Sub 64 G=0.73 A=0.27, T=0.00
Latin American 1 Sub 204 G=0.750 A=0.250, T=0.000
Latin American 2 Sub 832 G=0.782 A=0.218, T=0.000
South Asian Sub 136 G=0.794 A=0.206, T=0.000
Other Sub 3440 G=0.7605 A=0.2395, T=0.0000


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 264690 G=0.819411 A=0.180589
gnomAD - Genomes Global Study-wide 139878 G=0.824804 A=0.175196
gnomAD - Genomes European Sub 75752 G=0.76736 A=0.23264
gnomAD - Genomes African Sub 41984 G=0.95339 A=0.04661
gnomAD - Genomes American Sub 13568 G=0.79127 A=0.20873
gnomAD - Genomes Ashkenazi Jewish Sub 3318 G=0.7667 A=0.2333
gnomAD - Genomes East Asian Sub 3112 G=0.7227 A=0.2773
gnomAD - Genomes Other Sub 2144 G=0.7868 A=0.2132
Allele Frequency Aggregator Total Global 46284 G=0.77528 A=0.22472, T=0.00000
Allele Frequency Aggregator European Sub 36050 G=0.75207 A=0.24793, T=0.00000
Allele Frequency Aggregator African Sub 5154 G=0.9530 A=0.0470, T=0.0000
Allele Frequency Aggregator Other Sub 3440 G=0.7605 A=0.2395, T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 832 G=0.782 A=0.218, T=0.000
Allele Frequency Aggregator Asian Sub 468 G=0.707 A=0.293, T=0.000
Allele Frequency Aggregator Latin American 1 Sub 204 G=0.750 A=0.250, T=0.000
Allele Frequency Aggregator South Asian Sub 136 G=0.794 A=0.206, T=0.000
14KJPN JAPANESE Study-wide 28258 G=0.71236 A=0.28764
8.3KJPN JAPANESE Study-wide 16760 G=0.71217 A=0.28783
1000Genomes_30x Global Study-wide 4805 G=0.8298 A=0.1702
1000Genomes_30x African Sub 1328 G=0.9947 A=0.0053
1000Genomes_30x Europe Sub 961 G=0.717 A=0.283
1000Genomes_30x South Asian Sub 883 G=0.826 A=0.174
1000Genomes_30x East Asian Sub 878 G=0.708 A=0.292
1000Genomes_30x American Sub 755 G=0.829 A=0.171
1000Genomes Global Study-wide 3775 G=0.8257 A=0.1743
1000Genomes African Sub 1003 G=0.9940 A=0.0060
1000Genomes Europe Sub 766 G=0.714 A=0.286
1000Genomes East Asian Sub 764 G=0.711 A=0.289
1000Genomes South Asian Sub 718 G=0.830 A=0.170
1000Genomes American Sub 524 G=0.828 A=0.172
HapMap Global Study-wide 328 G=0.808 A=0.192
HapMap African Sub 120 G=1.000 A=0.000
HapMap American Sub 120 G=0.692 A=0.308
HapMap Asian Sub 88 G=0.70 A=0.30
SGDP_PRJ Global Study-wide 166 G=0.428 A=0.572
Qatari Global Study-wide 108 G=0.852 A=0.148
The Danish reference pan genome Danish Study-wide 40 G=0.72 A=0.28
A Vietnamese Genetic Variation Database Global Study-wide 30 G=0.90 A=0.10
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.p14 chr Y NC_000024.10:g.1614890G>A
GRCh38.p14 chr Y NC_000024.10:g.1614890G>T
GRCh37.p13 chr Y NC_000024.9:g.1683783G>A
GRCh37.p13 chr Y NC_000024.9:g.1683783G>T
ASMT RefSeqGene NG_016337.1:g.24436G>A
ASMT RefSeqGene NG_016337.1:g.24436G>T
GRCh38.p14 chr X NC_000023.11:g.1614890G>A
GRCh38.p14 chr X NC_000023.11:g.1614890G>T
GRCh37.p13 chr X NC_000023.10:g.1733783G>A
GRCh37.p13 chr X NC_000023.10:g.1733783G>T
Gene: ASMT, acetylserotonin O-methyltransferase (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ASMT transcript variant 2 NM_004043.3:c.-67-243G>A N/A Intron Variant
ASMT transcript variant 1 NM_001171038.2:c. N/A Genic Upstream Transcript Variant
ASMT transcript variant 3 NM_001171039.1:c. N/A Genic Upstream 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

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 G= A T
GRCh38.p14 chr Y NC_000024.10:g.1614890= NC_000024.10:g.1614890G>A NC_000024.10:g.1614890G>T
GRCh37.p13 chr Y NC_000024.9:g.1683783= NC_000024.9:g.1683783G>A NC_000024.9:g.1683783G>T
ASMT RefSeqGene NG_016337.1:g.24436= NG_016337.1:g.24436G>A NG_016337.1:g.24436G>T
GRCh38.p14 chr X NC_000023.11:g.1614890= NC_000023.11:g.1614890G>A NC_000023.11:g.1614890G>T
GRCh37.p13 chr X NC_000023.10:g.1733783= NC_000023.10:g.1733783G>A NC_000023.10:g.1733783G>T
ASMT transcript variant 2 NM_004043.2:c.-67-243= NM_004043.2:c.-67-243G>A NM_004043.2:c.-67-243G>T
ASMT transcript variant 2 NM_004043.3:c.-67-243= NM_004043.3:c.-67-243G>A NM_004043.3:c.-67-243G>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#.

64 SubSNP, 12 Frequency submissions
No Submitter Submission ID Date (Build)
1 SC_SNP ss8548439 Sep 28, 2016 (149)
2 PERLEGEN ss24100616 Sep 28, 2016 (149)
3 ABI ss43576358 Sep 28, 2016 (149)
4 PERLEGEN ss69256553 Sep 28, 2016 (149)
5 1000GENOMES ss112749021 Feb 14, 2009 (131)
6 ILLUMINA ss160680176 Dec 01, 2009 (131)
7 COMPLETE_GENOMICS ss162997312 Jul 04, 2010 (132)
8 COMPLETE_GENOMICS ss166019180 Jul 04, 2010 (132)
9 ILLUMINA ss173734869 Jul 04, 2010 (132)
10 ILLUMINA ss244299908 Jul 04, 2010 (132)
11 1000GENOMES ss341259917 May 09, 2011 (137)
12 ILLUMINA ss481935117 Sep 08, 2015 (146)
13 ILLUMINA ss482820935 May 04, 2012 (137)
14 ILLUMINA ss484352208 May 04, 2012 (137)
15 ILLUMINA ss534785118 Sep 08, 2015 (146)
16 ILLUMINA ss537236951 Sep 08, 2015 (146)
17 SSMP ss662666093 Apr 25, 2013 (138)
18 ILLUMINA ss779136359 Sep 08, 2015 (146)
19 ILLUMINA ss781888720 Sep 08, 2015 (146)
20 ILLUMINA ss834601006 Sep 08, 2015 (146)
21 JMKIDD_LAB ss1082755541 Aug 21, 2014 (142)
22 1000GENOMES ss1553292624 Apr 01, 2015 (144)
23 EVA_GENOME_DK ss1583307819 Apr 01, 2015 (144)
24 WEILL_CORNELL_DGM ss1939084171 Feb 12, 2016 (147)
25 ILLUMINA ss1958164001 Feb 12, 2016 (147)
26 GENOMED ss1971332912 Jul 19, 2016 (147)
27 ILLUMINA ss2094837512 Dec 20, 2016 (150)
28 ILLUMINA ss2095228808 Dec 20, 2016 (150)
29 SYSTEMSBIOZJU ss2629651941 Nov 08, 2017 (151)
30 ILLUMINA ss2634933261 Nov 08, 2017 (151)
31 GNOMAD ss2975943143 Nov 08, 2017 (151)
32 AFFY ss2986140586 Nov 08, 2017 (151)
33 SWEGEN ss3019544141 Nov 08, 2017 (151)
34 ILLUMINA ss3022984149 Nov 08, 2017 (151)
35 BIOINF_KMB_FNS_UNIBA ss3028992583 Nov 08, 2017 (151)
36 ILLUMINA ss3630387142 Oct 12, 2018 (152)
37 ILLUMINA ss3630503101 Oct 12, 2018 (152)
38 ILLUMINA ss3632820708 Oct 12, 2018 (152)
39 ILLUMINA ss3637013394 Oct 12, 2018 (152)
40 ILLUMINA ss3638885321 Oct 12, 2018 (152)
41 ILLUMINA ss3641265141 Oct 12, 2018 (152)
42 ILLUMINA ss3641563097 Oct 12, 2018 (152)
43 URBANLAB ss3651239655 Oct 12, 2018 (152)
44 ILLUMINA ss3653541910 Oct 12, 2018 (152)
45 ILLUMINA ss3653541911 Oct 12, 2018 (152)
46 ILLUMINA ss3726658378 Jul 14, 2019 (153)
47 EVA ss3769854459 Jul 14, 2019 (153)
48 KHV_HUMAN_GENOMES ss3822710998 Jul 14, 2019 (153)
49 EVA ss3836066067 Apr 27, 2020 (154)
50 SGDP_PRJ ss3890880471 Apr 27, 2020 (154)
51 EVA ss3984762711 Apr 26, 2021 (155)
52 GNOMAD ss4367069957 Apr 26, 2021 (155)
53 TOPMED ss5113778711 Apr 26, 2021 (155)
54 TOMMO_GENOMICS ss5233311860 Apr 26, 2021 (155)
55 1000G_HIGH_COVERAGE ss5311613336 Oct 17, 2022 (156)
56 EVA ss5316068691 Oct 17, 2022 (156)
57 HUGCELL_USP ss5503385680 Oct 17, 2022 (156)
58 1000G_HIGH_COVERAGE ss5619364353 Oct 17, 2022 (156)
59 SANFORD_IMAGENETICS ss5664778901 Oct 17, 2022 (156)
60 TOMMO_GENOMICS ss5794670840 Oct 17, 2022 (156)
61 YY_MCH ss5818842092 Oct 17, 2022 (156)
62 EVA ss5856992698 Oct 17, 2022 (156)
63 EVA ss5897815745 Oct 17, 2022 (156)
64 EVA ss5977726478 Oct 17, 2022 (156)
65 1000Genomes NC_000023.10 - 1733783 Oct 12, 2018 (152)
66 1000Genomes_30x NC_000023.11 - 1614890 Oct 17, 2022 (156)
67 The Danish reference pan genome NC_000023.10 - 1733783 Apr 27, 2020 (154)
68 gnomAD - Genomes NC_000023.11 - 1614890 Apr 26, 2021 (155)
69 HapMap NC_000024.10 - 1614890 Apr 27, 2020 (154)
70 Qatari NC_000023.10 - 1733783 Apr 27, 2020 (154)
71 SGDP_PRJ NC_000023.10 - 1733783 Apr 27, 2020 (154)
72 8.3KJPN NC_000023.10 - 1733783 Apr 26, 2021 (155)
73 14KJPN NC_000023.11 - 1614890 Oct 17, 2022 (156)
74 TopMed NC_000023.11 - 1614890 Apr 26, 2021 (155)
75 A Vietnamese Genetic Variation Database NC_000023.10 - 1733783 Jul 14, 2019 (153)
76 ALFA NC_000024.10 - 1614890 Apr 26, 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)
rs73174012 Dec 02, 2009 (131)
rs144667169 May 04, 2012 (137)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss112749021, ss162997312, ss166019180, ss484352208 NC_000023.9:1693782:G:A NC_000024.10:1614889:G:A (self)
81279536, 9472756, 21126093, 42897451, 91281167, 9911805, ss341259917, ss662666093, ss779136359, ss1082755541, ss1553292624, ss1583307819, ss1939084171, ss1958164001, ss1971332912, ss2629651941, ss2634933261, ss2975943143, ss3019544141, ss3022984149, ss3630387142, ss3632820708, ss3653541910, ss3653541911, ss3769854459, ss3836066067, ss3890880471, ss3984762711, ss5233311860, ss5316068691, ss5664778901, ss5977726478 NC_000023.10:1733782:G:A NC_000024.10:1614889:G:A (self)
106890288, 573878863, 128507944, 677385068, ss3028992583, ss3651239655, ss3726658378, ss3822710998, ss4367069957, ss5113778711, ss5311613336, ss5503385680, ss5619364353, ss5794670840, ss5818842092, ss5856992698, ss5897815745 NC_000023.11:1614889:G:A NC_000024.10:1614889:G:A (self)
ss481935117, ss482820935, ss534785118, ss537236951, ss781888720, ss834601006, ss2094837512, ss2095228808, ss2986140586, ss3630503101, ss3637013394, ss3638885321, ss3641265141, ss3641563097 NC_000024.9:1683782:G:A NC_000024.10:1614889:G:A (self)
4059992, 13528326425 NC_000024.10:1614889:G:A NC_000024.10:1614889:G:A (self)
ss8548439, ss24100616, ss43576358, ss69256553 NT_033330.5:235827:G:A NC_000024.10:1614889:G:A (self)
ss160680176, ss173734869, ss244299908 NT_167204.1:419548:G:A NC_000024.10:1614889:G:A (self)
13528326425 NC_000024.10:1614889:G:T NC_000024.10:1614889:G:T (self)
Help

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

6 citations for rs4446909
PMID Title Author Year Journal
17505466 Abnormal melatonin synthesis in autism spectrum disorders. Melke J et al. 2008 Molecular psychiatry
20377855 Mutation screening of melatonin-related genes in patients with autism spectrum disorders. Jonsson L et al. 2010 BMC medical genomics
20433639 Single-nucleotide polymorphisms and mRNA expression for melatonin synthesis rate-limiting enzyme in recurrent depressive disorder. Gałecki P et al. 2010 Journal of pineal research
21827647 Polymorphisms in melatonin synthesis pathways: possible influences on depression. Kripke DF et al. 2011 Journal of circadian rhythms
24308489 An ASMT variant associated with bipolar disorder influences sleep and circadian rhythms: a pilot study. Geoffroy PA et al. 2014 Genes, brain, and behavior
26322220 A comprehensive meta-analysis of common genetic variants in autism spectrum conditions. Warrier V et al. 2015 Molecular autism
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.post761+d5e8e07