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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.

rs1425948

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr15:57665116 (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.

Alleles
A>G
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.318297 (84250/264690, TOPMED)
A=0.325527 (45594/140062, GnomAD)
A=0.11505 (3251/28258, 14KJPN) (+ 17 more)
A=0.34115 (9132/26768, ALFA)
A=0.11283 (1891/16760, 8.3KJPN)
A=0.2826 (1810/6404, 1000G_30x)
A=0.2784 (1394/5008, 1000G)
A=0.3643 (1632/4480, Estonian)
A=0.3560 (1372/3854, ALSPAC)
A=0.3595 (1333/3708, TWINSUK)
A=0.1334 (391/2930, KOREAN)
A=0.2733 (517/1892, HapMap)
A=0.1135 (208/1832, Korea1K)
A=0.359 (358/998, GoNL)
A=0.375 (225/600, NorthernSweden)
A=0.211 (102/484, SGDP_PRJ)
A=0.231 (50/216, Qatari)
A=0.127 (27/212, Vietnamese)
A=0.22 (12/54, Siberian)
A=0.30 (12/40, GENOME_DK)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GCOM1 : Intron Variant
MYZAP : Intron Variant
Publications
0 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 26768 A=0.34115 G=0.65885
European Sub 17000 A=0.35082 G=0.64918
African Sub 4710 A=0.2911 G=0.7089
African Others Sub 154 A=0.292 G=0.708
African American Sub 4556 A=0.2910 G=0.7090
Asian Sub 168 A=0.143 G=0.857
East Asian Sub 110 A=0.109 G=0.891
Other Asian Sub 58 A=0.21 G=0.79
Latin American 1 Sub 314 A=0.334 G=0.666
Latin American 2 Sub 2830 A=0.3830 G=0.6170
South Asian Sub 106 A=0.236 G=0.764
Other Sub 1640 A=0.3409 G=0.6591


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 A=0.318297 G=0.681703
gnomAD - Genomes Global Study-wide 140062 A=0.325527 G=0.674473
gnomAD - Genomes European Sub 75858 A=0.35676 G=0.64324
gnomAD - Genomes African Sub 41958 A=0.28912 G=0.71088
gnomAD - Genomes American Sub 13648 A=0.33155 G=0.66845
gnomAD - Genomes Ashkenazi Jewish Sub 3320 A=0.2283 G=0.7717
gnomAD - Genomes East Asian Sub 3126 A=0.1276 G=0.8724
gnomAD - Genomes Other Sub 2152 A=0.3336 G=0.6664
14KJPN JAPANESE Study-wide 28258 A=0.11505 G=0.88495
Allele Frequency Aggregator Total Global 26768 A=0.34115 G=0.65885
Allele Frequency Aggregator European Sub 17000 A=0.35082 G=0.64918
Allele Frequency Aggregator African Sub 4710 A=0.2911 G=0.7089
Allele Frequency Aggregator Latin American 2 Sub 2830 A=0.3830 G=0.6170
Allele Frequency Aggregator Other Sub 1640 A=0.3409 G=0.6591
Allele Frequency Aggregator Latin American 1 Sub 314 A=0.334 G=0.666
Allele Frequency Aggregator Asian Sub 168 A=0.143 G=0.857
Allele Frequency Aggregator South Asian Sub 106 A=0.236 G=0.764
8.3KJPN JAPANESE Study-wide 16760 A=0.11283 G=0.88717
1000Genomes_30x Global Study-wide 6404 A=0.2826 G=0.7174
1000Genomes_30x African Sub 1786 A=0.2592 G=0.7408
1000Genomes_30x Europe Sub 1266 A=0.3641 G=0.6359
1000Genomes_30x South Asian Sub 1202 A=0.2795 G=0.7205
1000Genomes_30x East Asian Sub 1170 A=0.1393 G=0.8607
1000Genomes_30x American Sub 980 A=0.395 G=0.605
1000Genomes Global Study-wide 5008 A=0.2784 G=0.7216
1000Genomes African Sub 1322 A=0.2708 G=0.7292
1000Genomes East Asian Sub 1008 A=0.1310 G=0.8690
1000Genomes Europe Sub 1006 A=0.3539 G=0.6461
1000Genomes South Asian Sub 978 A=0.280 G=0.720
1000Genomes American Sub 694 A=0.395 G=0.605
Genetic variation in the Estonian population Estonian Study-wide 4480 A=0.3643 G=0.6357
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 A=0.3560 G=0.6440
UK 10K study - Twins TWIN COHORT Study-wide 3708 A=0.3595 G=0.6405
KOREAN population from KRGDB KOREAN Study-wide 2930 A=0.1334 G=0.8666
HapMap Global Study-wide 1892 A=0.2733 G=0.7267
HapMap American Sub 770 A=0.292 G=0.708
HapMap African Sub 692 A=0.314 G=0.686
HapMap Asian Sub 254 A=0.102 G=0.898
HapMap Europe Sub 176 A=0.278 G=0.722
Korean Genome Project KOREAN Study-wide 1832 A=0.1135 G=0.8865
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 A=0.359 G=0.641
Northern Sweden ACPOP Study-wide 600 A=0.375 G=0.625
SGDP_PRJ Global Study-wide 484 A=0.211 G=0.789
Qatari Global Study-wide 216 A=0.231 G=0.769
A Vietnamese Genetic Variation Database Global Study-wide 212 A=0.127 G=0.873
Siberian Global Study-wide 54 A=0.22 G=0.78
The Danish reference pan genome Danish Study-wide 40 A=0.30 G=0.70
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 15 NC_000015.10:g.57665116A>G
GRCh37.p13 chr 15 NC_000015.9:g.57957314A>G
Gene: GCOM1, GCOM1, MYZAP-POLR2M combined locus (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GCOM1 transcript variant 1 NM_001018090.6:c.1203+358…

NM_001018090.6:c.1203+3583A>G

 		N/A Intron Variant
GCOM1 transcript variant 2 NM_001018091.6:c.1203+358…

NM_001018091.6:c.1203+3583A>G

 		N/A Intron Variant
GCOM1 transcript variant 14 NM_001285900.3:c.1203+358…

NM_001285900.3:c.1203+3583A>G

 		N/A Intron Variant
GCOM1 transcript variant 10 NR_104367.2:n. N/A Intron Variant
GCOM1 transcript variant 3 NR_104368.2:n. N/A Intron Variant
GCOM1 transcript variant 4 NR_104369.2:n. N/A Intron Variant
GCOM1 transcript variant 5 NR_104370.2:n. N/A Intron Variant
GCOM1 transcript variant 9 NR_104371.3:n. N/A Intron Variant
Gene: MYZAP, myocardial zonula adherens protein (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MYZAP transcript variant 1 NM_001018100.5:c.1203+358…

NM_001018100.5:c.1203+3583A>G

 		N/A Intron Variant
MYZAP transcript variant 2 NM_152451.8:c.1120-9852A>G 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

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= G
GRCh38.p14 chr 15 NC_000015.10:g.57665116= NC_000015.10:g.57665116A>G
GRCh37.p13 chr 15 NC_000015.9:g.57957314= NC_000015.9:g.57957314A>G
GCOM1 transcript variant 1 NM_001018090.4:c.1203+3583= NM_001018090.4:c.1203+3583A>G
GCOM1 transcript variant 1 NM_001018090.6:c.1203+3583= NM_001018090.6:c.1203+3583A>G
GCOM1 transcript variant 2 NM_001018091.4:c.1203+3583= NM_001018091.4:c.1203+3583A>G
GCOM1 transcript variant 2 NM_001018091.6:c.1203+3583= NM_001018091.6:c.1203+3583A>G
MYZAP transcript variant 1 NM_001018100.3:c.1203+3583= NM_001018100.3:c.1203+3583A>G
MYZAP transcript variant 1 NM_001018100.5:c.1203+3583= NM_001018100.5:c.1203+3583A>G
GCOM1 transcript variant 14 NM_001285900.3:c.1203+3583= NM_001285900.3:c.1203+3583A>G
MYZAP transcript variant 2 NM_152451.6:c.1120-9852= NM_152451.6:c.1120-9852A>G
MYZAP transcript variant 2 NM_152451.8:c.1120-9852= NM_152451.8:c.1120-9852A>G
MYZAP transcript variant X1 XM_005254109.1:c.1158+3583= XM_005254109.1:c.1158+3583A>G
MYZAP transcript variant X2 XM_005254110.1:c.1110+3583= XM_005254110.1:c.1110+3583A>G
MYZAP transcript variant X3 XM_005254111.1:c.996+3583= XM_005254111.1:c.996+3583A>G
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#.

91 SubSNP, 20 Frequency submissions
No Submitter Submission ID Date (Build)
1 TSC-CSHL ss2232726 Oct 23, 2000 (88)
2 WI_SSAHASNP ss6586631 Feb 20, 2003 (111)
3 BCM_SSAHASNP ss14159883 Dec 05, 2003 (119)
4 CSHL-HAPMAP ss17551775 Feb 27, 2004 (120)
5 SSAHASNP ss21300326 Apr 05, 2004 (121)
6 PERLEGEN ss24613893 Sep 20, 2004 (123)
7 ABI ss43697442 Mar 15, 2006 (126)
8 ILLUMINA ss65775284 Oct 13, 2006 (127)
9 AFFY ss66438514 Nov 29, 2006 (127)
10 ILLUMINA ss74979654 Dec 07, 2007 (129)
11 AFFY ss76217778 Dec 08, 2007 (130)
12 KRIBB_YJKIM ss81477321 Dec 14, 2007 (130)
13 BCMHGSC_JDW ss90171139 Mar 24, 2008 (129)
14 HUMANGENOME_JCVI ss96814385 Feb 05, 2009 (130)
15 BGI ss106432233 Feb 05, 2009 (130)
16 1000GENOMES ss108851389 Jan 23, 2009 (130)
17 1000GENOMES ss114235353 Jan 25, 2009 (130)
18 ILLUMINA-UK ss118242885 Feb 14, 2009 (130)
19 ENSEMBL ss136366382 Dec 01, 2009 (131)
20 ENSEMBL ss136891964 Dec 01, 2009 (131)
21 GMI ss156593691 Dec 01, 2009 (131)
22 COMPLETE_GENOMICS ss168090787 Jul 04, 2010 (132)
23 COMPLETE_GENOMICS ss169594381 Jul 04, 2010 (132)
24 COMPLETE_GENOMICS ss171165771 Jul 04, 2010 (132)
25 ILLUMINA ss172492372 Jul 04, 2010 (132)
26 AFFY ss172850752 Jul 04, 2010 (132)
27 BUSHMAN ss200893596 Jul 04, 2010 (132)
28 BCM-HGSC-SUB ss207247222 Jul 04, 2010 (132)
29 1000GENOMES ss226914851 Jul 14, 2010 (132)
30 1000GENOMES ss236794769 Jul 15, 2010 (132)
31 1000GENOMES ss243179097 Jul 15, 2010 (132)
32 BL ss255018495 May 09, 2011 (134)
33 GMI ss282273824 May 04, 2012 (137)
34 PJP ss291729075 May 09, 2011 (134)
35 ILLUMINA ss536869682 Sep 08, 2015 (146)
36 TISHKOFF ss564506617 Apr 25, 2013 (138)
37 SSMP ss660236520 Apr 25, 2013 (138)
38 EVA-GONL ss991831458 Aug 21, 2014 (142)
39 JMKIDD_LAB ss1080160902 Aug 21, 2014 (142)
40 1000GENOMES ss1353636601 Aug 21, 2014 (142)
41 DDI ss1427639552 Apr 01, 2015 (144)
42 EVA_GENOME_DK ss1577643099 Apr 01, 2015 (144)
43 EVA_UK10K_ALSPAC ss1633088703 Apr 01, 2015 (144)
44 EVA_UK10K_TWINSUK ss1676082736 Apr 01, 2015 (144)
45 EVA_DECODE ss1695851072 Apr 01, 2015 (144)
46 EVA_SVP ss1713493116 Apr 01, 2015 (144)
47 HAMMER_LAB ss1808224183 Sep 08, 2015 (146)
48 WEILL_CORNELL_DGM ss1935237077 Feb 12, 2016 (147)
49 GENOMED ss1968119202 Jul 19, 2016 (147)
50 JJLAB ss2028398923 Sep 14, 2016 (149)
51 USC_VALOUEV ss2156802870 Dec 20, 2016 (150)
52 HUMAN_LONGEVITY ss2207135916 Dec 20, 2016 (150)
53 SYSTEMSBIOZJU ss2628694025 Nov 08, 2017 (151)
54 GRF ss2701275100 Nov 08, 2017 (151)
55 GNOMAD ss2935395470 Nov 08, 2017 (151)
56 SWEGEN ss3013354049 Nov 08, 2017 (151)
57 BIOINF_KMB_FNS_UNIBA ss3028023173 Nov 08, 2017 (151)
58 CSHL ss3351136079 Nov 08, 2017 (151)
59 ILLUMINA ss3627370365 Oct 12, 2018 (152)
60 ILLUMINA ss3638088011 Oct 12, 2018 (152)
61 ILLUMINA ss3643072164 Oct 12, 2018 (152)
62 URBANLAB ss3650363454 Oct 12, 2018 (152)
63 EGCUT_WGS ss3680497519 Jul 13, 2019 (153)
64 EVA_DECODE ss3697976357 Jul 13, 2019 (153)
65 ACPOP ss3740962297 Jul 13, 2019 (153)
66 EVA ss3753139951 Jul 13, 2019 (153)
67 PACBIO ss3787859113 Jul 13, 2019 (153)
68 PACBIO ss3792869119 Jul 13, 2019 (153)
69 PACBIO ss3797753690 Jul 13, 2019 (153)
70 KHV_HUMAN_GENOMES ss3818457060 Jul 13, 2019 (153)
71 EVA ss3834257707 Apr 27, 2020 (154)
72 EVA ss3840727692 Apr 27, 2020 (154)
73 EVA ss3846216574 Apr 27, 2020 (154)
74 SGDP_PRJ ss3883008210 Apr 27, 2020 (154)
75 KRGDB ss3932185953 Apr 27, 2020 (154)
76 KOGIC ss3976227287 Apr 27, 2020 (154)
77 EVA ss4017704006 Apr 26, 2021 (155)
78 TOPMED ss4992900015 Apr 26, 2021 (155)
79 TOMMO_GENOMICS ss5216393912 Apr 26, 2021 (155)
80 1000G_HIGH_COVERAGE ss5298593224 Oct 16, 2022 (156)
81 EVA ss5419507784 Oct 16, 2022 (156)
82 HUGCELL_USP ss5492304770 Oct 16, 2022 (156)
83 EVA ss5511448596 Oct 16, 2022 (156)
84 1000G_HIGH_COVERAGE ss5600073077 Oct 16, 2022 (156)
85 SANFORD_IMAGENETICS ss5657597936 Oct 16, 2022 (156)
86 TOMMO_GENOMICS ss5770257264 Oct 16, 2022 (156)
87 YY_MCH ss5815374400 Oct 16, 2022 (156)
88 EVA ss5828260131 Oct 16, 2022 (156)
89 EVA ss5851312314 Oct 16, 2022 (156)
90 EVA ss5876049723 Oct 16, 2022 (156)
91 EVA ss5949001514 Oct 16, 2022 (156)
92 1000Genomes NC_000015.9 - 57957314 Oct 12, 2018 (152)
93 1000Genomes_30x NC_000015.10 - 57665116 Oct 16, 2022 (156)
94 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 57957314 Oct 12, 2018 (152)
95 Genetic variation in the Estonian population NC_000015.9 - 57957314 Oct 12, 2018 (152)
96 The Danish reference pan genome NC_000015.9 - 57957314 Apr 27, 2020 (154)
97 gnomAD - Genomes NC_000015.10 - 57665116 Apr 26, 2021 (155)
98 Genome of the Netherlands Release 5 NC_000015.9 - 57957314 Apr 27, 2020 (154)
99 HapMap NC_000015.10 - 57665116 Apr 27, 2020 (154)
100 KOREAN population from KRGDB NC_000015.9 - 57957314 Apr 27, 2020 (154)
101 Korean Genome Project NC_000015.10 - 57665116 Apr 27, 2020 (154)
102 Northern Sweden NC_000015.9 - 57957314 Jul 13, 2019 (153)
103 Qatari NC_000015.9 - 57957314 Apr 27, 2020 (154)
104 SGDP_PRJ NC_000015.9 - 57957314 Apr 27, 2020 (154)
105 Siberian NC_000015.9 - 57957314 Apr 27, 2020 (154)
106 8.3KJPN NC_000015.9 - 57957314 Apr 26, 2021 (155)
107 14KJPN NC_000015.10 - 57665116 Oct 16, 2022 (156)
108 TopMed NC_000015.10 - 57665116 Apr 26, 2021 (155)
109 UK 10K study - Twins NC_000015.9 - 57957314 Oct 12, 2018 (152)
110 A Vietnamese Genetic Variation Database NC_000015.9 - 57957314 Jul 13, 2019 (153)
111 ALFA NC_000015.10 - 57665116 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)
rs17240041 Oct 08, 2004 (123)
rs56543722 May 25, 2008 (130)
rs56952086 Feb 26, 2009 (130)
Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss90171139, ss108851389, ss114235353, ss118242885, ss168090787, ss169594381, ss171165771, ss200893596, ss207247222, ss255018495, ss282273824, ss291729075, ss1695851072, ss1713493116, ss3643072164 NC_000015.8:55744605:A:G NC_000015.10:57665115:A:G (self)
66714783, 37036263, 26235767, 3875428, 16538751, 39363347, 14247162, 17279007, 35025190, 9319224, 74363219, 37036263, 8241533, ss226914851, ss236794769, ss243179097, ss536869682, ss564506617, ss660236520, ss991831458, ss1080160902, ss1353636601, ss1427639552, ss1577643099, ss1633088703, ss1676082736, ss1808224183, ss1935237077, ss1968119202, ss2028398923, ss2156802870, ss2628694025, ss2701275100, ss2935395470, ss3013354049, ss3351136079, ss3627370365, ss3638088011, ss3680497519, ss3740962297, ss3753139951, ss3787859113, ss3792869119, ss3797753690, ss3834257707, ss3840727692, ss3883008210, ss3932185953, ss4017704006, ss5216393912, ss5419507784, ss5511448596, ss5657597936, ss5828260131, ss5949001514 NC_000015.9:57957313:A:G NC_000015.10:57665115:A:G (self)
87599012, 470325937, 1272495, 32605288, 104094368, 208445675, 4810790251, ss2207135916, ss3028023173, ss3650363454, ss3697976357, ss3818457060, ss3846216574, ss3976227287, ss4992900015, ss5298593224, ss5492304770, ss5600073077, ss5770257264, ss5815374400, ss5851312314, ss5876049723 NC_000015.10:57665115:A:G NC_000015.10:57665115:A:G (self)
ss14159883, ss17551775, ss21300326 NT_010194.16:28747870:A:G NC_000015.10:57665115:A:G (self)
ss2232726, ss6586631, ss24613893, ss43697442, ss65775284, ss66438514, ss74979654, ss76217778, ss81477321, ss96814385, ss106432233, ss136366382, ss136891964, ss156593691, ss172492372, ss172850752 NT_010194.17:28747870:A:G NC_000015.10:57665115: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.

No publications for rs1425948

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