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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.

rs185027625

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr4:119186601 (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
G>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.003940 (1043/264690, TOPMED)
T=0.003945 (553/140174, GnomAD)
T=0.00408 (77/18890, ALFA) (+ 7 more)
T=0.0017 (11/6404, 1000G_30x)
T=0.0010 (5/5008, 1000G)
T=0.0029 (13/4480, Estonian)
T=0.0080 (31/3854, ALSPAC)
T=0.0076 (28/3708, TWINSUK)
T=0.006 (6/998, GoNL)
T=0.003 (2/600, NorthernSweden)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
MYOZ2 : 3 Prime UTR 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 18890 G=0.99592 T=0.00408
European Sub 14286 G=0.99496 T=0.00504
African Sub 2946 G=0.9993 T=0.0007
African Others Sub 114 G=1.000 T=0.000
African American Sub 2832 G=0.9993 T=0.0007
Asian Sub 112 G=1.000 T=0.000
East Asian Sub 86 G=1.00 T=0.00
Other Asian Sub 26 G=1.00 T=0.00
Latin American 1 Sub 146 G=1.000 T=0.000
Latin American 2 Sub 610 G=0.997 T=0.003
South Asian Sub 98 G=1.00 T=0.00
Other Sub 692 G=0.999 T=0.001


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=0.996060 T=0.003940
gnomAD - Genomes Global Study-wide 140174 G=0.996055 T=0.003945
gnomAD - Genomes European Sub 75910 G=0.99381 T=0.00619
gnomAD - Genomes African Sub 42006 G=0.99905 T=0.00095
gnomAD - Genomes American Sub 13658 G=0.99780 T=0.00220
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9991 T=0.0009
gnomAD - Genomes East Asian Sub 3130 G=1.0000 T=0.0000
gnomAD - Genomes Other Sub 2146 G=0.9953 T=0.0047
Allele Frequency Aggregator Total Global 18890 G=0.99592 T=0.00408
Allele Frequency Aggregator European Sub 14286 G=0.99496 T=0.00504
Allele Frequency Aggregator African Sub 2946 G=0.9993 T=0.0007
Allele Frequency Aggregator Other Sub 692 G=0.999 T=0.001
Allele Frequency Aggregator Latin American 2 Sub 610 G=0.997 T=0.003
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 112 G=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 T=0.00
1000Genomes_30x Global Study-wide 6404 G=0.9983 T=0.0017
1000Genomes_30x African Sub 1786 G=0.9994 T=0.0006
1000Genomes_30x Europe Sub 1266 G=0.9961 T=0.0039
1000Genomes_30x South Asian Sub 1202 G=1.0000 T=0.0000
1000Genomes_30x East Asian Sub 1170 G=1.0000 T=0.0000
1000Genomes_30x American Sub 980 G=0.995 T=0.005
1000Genomes Global Study-wide 5008 G=0.9990 T=0.0010
1000Genomes African Sub 1322 G=0.9992 T=0.0008
1000Genomes East Asian Sub 1008 G=1.0000 T=0.0000
1000Genomes Europe Sub 1006 G=0.9970 T=0.0030
1000Genomes South Asian Sub 978 G=1.000 T=0.000
1000Genomes American Sub 694 G=0.999 T=0.001
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9971 T=0.0029
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9920 T=0.0080
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9924 T=0.0076
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.994 T=0.006
Northern Sweden ACPOP Study-wide 600 G=0.997 T=0.003
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 4 NC_000004.12:g.119186601G>T
GRCh37.p13 chr 4 NC_000004.11:g.120107756G>T
MYOZ2 RefSeqGene (LRG_396) NG_029747.1:g.55818G>T
Gene: MYOZ2, myozenin 2 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
MYOZ2 transcript NM_016599.5:c.*401= N/A 3 Prime UTR Variant
MYOZ2 transcript variant X1 XM_006714234.5:c. 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

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= T
GRCh38.p14 chr 4 NC_000004.12:g.119186601= NC_000004.12:g.119186601G>T
GRCh37.p13 chr 4 NC_000004.11:g.120107756= NC_000004.11:g.120107756G>T
MYOZ2 RefSeqGene (LRG_396) NG_029747.1:g.55818= NG_029747.1:g.55818G>T
MYOZ2 transcript NM_016599.5:c.*401= NM_016599.5:c.*401G>T
MYOZ2 transcript NM_016599.4:c.*401= NM_016599.4:c.*401G>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#.

23 SubSNP, 10 Frequency submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss457413755 Sep 17, 2011 (135)
2 EVA-GONL ss980596739 Aug 21, 2014 (142)
3 JMKIDD_LAB ss1071896537 Aug 21, 2014 (142)
4 1000GENOMES ss1311522153 Aug 21, 2014 (142)
5 EVA_DECODE ss1590104269 Apr 01, 2015 (144)
6 EVA_UK10K_ALSPAC ss1611023591 Apr 01, 2015 (144)
7 EVA_UK10K_TWINSUK ss1654017624 Apr 01, 2015 (144)
8 HUMAN_LONGEVITY ss2266549897 Dec 20, 2016 (150)
9 GNOMAD ss2814421367 Nov 08, 2017 (151)
10 SWEGEN ss2995433820 Nov 08, 2017 (151)
11 CSHL ss3345925269 Nov 08, 2017 (151)
12 EGCUT_WGS ss3663336149 Jul 13, 2019 (153)
13 EVA_DECODE ss3712921415 Jul 13, 2019 (153)
14 ACPOP ss3731542513 Jul 13, 2019 (153)
15 TOPMED ss4629449974 Apr 26, 2021 (155)
16 1000G_HIGH_COVERAGE ss5260765435 Oct 17, 2022 (156)
17 EVA ss5351831848 Oct 17, 2022 (156)
18 HUGCELL_USP ss5459352744 Oct 17, 2022 (156)
19 1000G_HIGH_COVERAGE ss5542688145 Oct 17, 2022 (156)
20 SANFORD_IMAGENETICS ss5635940475 Oct 17, 2022 (156)
21 EVA ss5844609870 Oct 17, 2022 (156)
22 EVA ss5865215406 Oct 17, 2022 (156)
23 EVA ss5964341505 Oct 17, 2022 (156)
24 1000Genomes NC_000004.11 - 120107756 Oct 12, 2018 (152)
25 1000Genomes_30x NC_000004.12 - 119186601 Oct 17, 2022 (156)
26 The Avon Longitudinal Study of Parents and Children NC_000004.11 - 120107756 Oct 12, 2018 (152)
27 Genetic variation in the Estonian population NC_000004.11 - 120107756 Oct 12, 2018 (152)
28 gnomAD - Genomes NC_000004.12 - 119186601 Apr 26, 2021 (155)
29 Genome of the Netherlands Release 5 NC_000004.11 - 120107756 Apr 26, 2020 (154)
30 Northern Sweden NC_000004.11 - 120107756 Jul 13, 2019 (153)
31 TopMed NC_000004.12 - 119186601 Apr 26, 2021 (155)
32 UK 10K study - Twins NC_000004.11 - 120107756 Oct 12, 2018 (152)
33 ALFA NC_000004.12 - 119186601 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).

Added to this RefSNP Cluster:
Submission IDs Observation SPDI Canonical SPDI Source RSIDs
ss1590104269 NC_000004.10:120327203:G:T NC_000004.12:119186600:G:T (self)
22985751, 12788034, 9074397, 5656688, 4827378, 12788034, ss457413755, ss980596739, ss1071896537, ss1311522153, ss1611023591, ss1654017624, ss2814421367, ss2995433820, ss3345925269, ss3663336149, ss3731542513, ss5351831848, ss5635940475, ss5844609870, ss5964341505 NC_000004.11:120107755:G:T NC_000004.12:119186600:G:T (self)
30214080, 162843438, 466827530, 11065387732, ss2266549897, ss3712921415, ss4629449974, ss5260765435, ss5459352744, ss5542688145, ss5865215406 NC_000004.12:119186600:G:T NC_000004.12:119186600: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.

No publications for rs185027625

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