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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.

rs121912701

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:51989026 (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>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.002962 (784/264690, TOPMED)
A=0.003672 (921/250836, GnomAD_exome)
A=0.004994 (1026/205466, ALFA) (+ 14 more)
A=0.003452 (484/140204, GnomAD)
A=0.003988 (482/120860, ExAC)
A=0.00112 (88/78696, PAGE_STUDY)
A=0.0028 (18/6404, 1000G_30x)
A=0.0028 (14/5008, 1000G)
A=0.0038 (17/4480, Estonian)
A=0.0054 (21/3854, ALSPAC)
A=0.0049 (18/3708, TWINSUK)
A=0.012 (12/998, GoNL)
A=0.010 (6/600, NorthernSweden)
A=0.006 (3/534, MGP)
A=0.010 (3/304, FINRISK)
G=0.5 (1/2, SGDP_PRJ)
A=0.5 (1/2, SGDP_PRJ)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ABHD14A-ACY1 : Missense Variant
ACY1 : Missense Variant
Publications
2 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 221972 G=0.995148 A=0.004852
European Sub 186282 G=0.994669 A=0.005331
African Sub 9806 G=0.9988 A=0.0012
African Others Sub 360 G=1.000 A=0.000
African American Sub 9446 G=0.9987 A=0.0013
Asian Sub 6350 G=0.9998 A=0.0002
East Asian Sub 4502 G=1.0000 A=0.0000
Other Asian Sub 1848 G=0.9995 A=0.0005
Latin American 1 Sub 796 G=0.999 A=0.001
Latin American 2 Sub 968 G=0.997 A=0.003
South Asian Sub 280 G=1.000 A=0.000
Other Sub 17490 G=0.99617 A=0.00383


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=0.997038 A=0.002962
gnomAD - Exomes Global Study-wide 250836 G=0.996328 A=0.003672
gnomAD - Exomes European Sub 134840 G=0.994423 A=0.005577
gnomAD - Exomes Asian Sub 49006 G=0.99969 A=0.00031
gnomAD - Exomes American Sub 34584 G=0.99850 A=0.00150
gnomAD - Exomes African Sub 16220 G=0.99945 A=0.00055
gnomAD - Exomes Ashkenazi Jewish Sub 10058 G=0.99334 A=0.00666
gnomAD - Exomes Other Sub 6128 G=0.9958 A=0.0042
Allele Frequency Aggregator Total Global 205466 G=0.995006 A=0.004994
Allele Frequency Aggregator European Sub 176066 G=0.994599 A=0.005401
Allele Frequency Aggregator Other Sub 16038 G=0.99601 A=0.00399
Allele Frequency Aggregator Asian Sub 6350 G=0.9998 A=0.0002
Allele Frequency Aggregator African Sub 4968 G=0.9988 A=0.0012
Allele Frequency Aggregator Latin American 2 Sub 968 G=0.997 A=0.003
Allele Frequency Aggregator Latin American 1 Sub 796 G=0.999 A=0.001
Allele Frequency Aggregator South Asian Sub 280 G=1.000 A=0.000
gnomAD - Genomes Global Study-wide 140204 G=0.996548 A=0.003452
gnomAD - Genomes European Sub 75930 G=0.99472 A=0.00528
gnomAD - Genomes African Sub 42010 G=0.99917 A=0.00083
gnomAD - Genomes American Sub 13654 G=0.99868 A=0.00132
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=0.9919 A=0.0081
gnomAD - Genomes East Asian Sub 3132 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=0.9986 A=0.0014
ExAC Global Study-wide 120860 G=0.996012 A=0.003988
ExAC Europe Sub 73056 G=0.99384 A=0.00616
ExAC Asian Sub 25098 G=0.99964 A=0.00036
ExAC American Sub 11540 G=0.99879 A=0.00121
ExAC African Sub 10264 G=0.99942 A=0.00058
ExAC Other Sub 902 G=0.997 A=0.003
The PAGE Study Global Study-wide 78696 G=0.99888 A=0.00112
The PAGE Study AfricanAmerican Sub 32510 G=0.99914 A=0.00086
The PAGE Study Mexican Sub 10810 G=0.99759 A=0.00241
The PAGE Study Asian Sub 8318 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7918 G=0.9992 A=0.0008
The PAGE Study NativeHawaiian Sub 4534 G=0.9985 A=0.0015
The PAGE Study Cuban Sub 4230 G=0.9986 A=0.0014
The PAGE Study Dominican Sub 3828 G=0.9990 A=0.0010
The PAGE Study CentralAmerican Sub 2450 G=0.9988 A=0.0012
The PAGE Study SouthAmerican Sub 1982 G=0.9980 A=0.0020
The PAGE Study NativeAmerican Sub 1260 G=0.9968 A=0.0032
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
1000Genomes_30x Global Study-wide 6404 G=0.9972 A=0.0028
1000Genomes_30x African Sub 1786 G=0.9989 A=0.0011
1000Genomes_30x Europe Sub 1266 G=0.9929 A=0.0071
1000Genomes_30x South Asian Sub 1202 G=0.9992 A=0.0008
1000Genomes_30x East Asian Sub 1170 G=1.0000 A=0.0000
1000Genomes_30x American Sub 980 G=0.994 A=0.006
1000Genomes Global Study-wide 5008 G=0.9972 A=0.0028
1000Genomes African Sub 1322 G=0.9992 A=0.0008
1000Genomes East Asian Sub 1008 G=1.0000 A=0.0000
1000Genomes Europe Sub 1006 G=0.9911 A=0.0089
1000Genomes South Asian Sub 978 G=0.999 A=0.001
1000Genomes American Sub 694 G=0.996 A=0.004
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9962 A=0.0038
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.9946 A=0.0054
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.9951 A=0.0049
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 G=0.988 A=0.012
Northern Sweden ACPOP Study-wide 600 G=0.990 A=0.010
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 G=0.994 A=0.006
FINRISK Finnish from FINRISK project Study-wide 304 G=0.990 A=0.010
SGDP_PRJ Global Study-wide 2 G=0.5 A=0.5
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 3 NC_000003.12:g.51989026G>A
GRCh37.p13 chr 3 NC_000003.11:g.52023042G>A
ACY1 RefSeqGene NG_012036.1:g.10480G>A
Gene: ACY1, aminoacylase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ACY1 transcript variant 1 NM_000666.3:c.1178G>A R [CGC] > H [CAC] Coding Sequence Variant
aminoacylase-1 isoform a NP_000657.1:p.Arg393His R (Arg) > H (His) Missense Variant
ACY1 transcript variant 3 NM_001198896.2:c.962G>A R [CGC] > H [CAC] Coding Sequence Variant
aminoacylase-1 isoform b NP_001185825.1:p.Arg321His R (Arg) > H (His) Missense Variant
ACY1 transcript variant 2 NM_001198895.2:c.1178G>A R [CGC] > H [CAC] Coding Sequence Variant
aminoacylase-1 isoform a NP_001185824.1:p.Arg393His R (Arg) > H (His) Missense Variant
ACY1 transcript variant 5 NM_001198898.2:c.1073G>A R [CGC] > H [CAC] Coding Sequence Variant
aminoacylase-1 isoform d NP_001185827.1:p.Arg358His R (Arg) > H (His) Missense Variant
ACY1 transcript variant 4 NM_001198897.2:c.983G>A R [CGC] > H [CAC] Coding Sequence Variant
aminoacylase-1 isoform c NP_001185826.1:p.Arg328His R (Arg) > H (His) Missense Variant
Gene: ABHD14A-ACY1, ABHD14A-ACY1 readthrough (plus strand)
Molecule type Change Amino acid[Codon] SO Term
ABHD14A-ACY1 transcript NM_001316331.2:c.1448G>A R [CGC] > H [CAC] Coding Sequence Variant
ABHD14A-ACY1 readthrough (NMD candidate) NP_001303260.1:p.Arg483His R (Arg) > H (His) Missense 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.

Allele: A (allele ID: 33153 )
ClinVar Accession Disease Names Clinical Significance
RCV000019742.29 Aminoacylase 1 deficiency Pathogenic
RCV000292281.3 not specified Benign
RCV000488111.13 not provided Conflicting-Interpretations-Of-Pathogenicity
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
GRCh38.p14 chr 3 NC_000003.12:g.51989026= NC_000003.12:g.51989026G>A
GRCh37.p13 chr 3 NC_000003.11:g.52023042= NC_000003.11:g.52023042G>A
ACY1 RefSeqGene NG_012036.1:g.10480= NG_012036.1:g.10480G>A
ACY1 transcript variant 1 NM_000666.3:c.1178= NM_000666.3:c.1178G>A
ACY1 transcript variant 1 NM_000666.2:c.1178= NM_000666.2:c.1178G>A
ACY1 transcript variant 2 NM_001198895.2:c.1178= NM_001198895.2:c.1178G>A
ACY1 transcript variant 2 NM_001198895.1:c.1178= NM_001198895.1:c.1178G>A
ACY1 transcript variant 5 NM_001198898.2:c.1073= NM_001198898.2:c.1073G>A
ACY1 transcript variant 5 NM_001198898.1:c.1073= NM_001198898.1:c.1073G>A
ACY1 transcript variant 4 NM_001198897.2:c.983= NM_001198897.2:c.983G>A
ACY1 transcript variant 4 NM_001198897.1:c.983= NM_001198897.1:c.983G>A
ACY1 transcript variant 3 NM_001198896.2:c.962= NM_001198896.2:c.962G>A
ACY1 transcript variant 3 NM_001198896.1:c.962= NM_001198896.1:c.962G>A
ABHD14A-ACY1 transcript NM_001316331.2:c.1448= NM_001316331.2:c.1448G>A
ABHD14A-ACY1 transcript NM_001316331.1:c.1448= NM_001316331.1:c.1448G>A
ABHD14A-ACY1 transcript NR_037192.1:n.1703= NR_037192.1:n.1703G>A
aminoacylase-1 isoform a NP_000657.1:p.Arg393= NP_000657.1:p.Arg393His
aminoacylase-1 isoform a NP_001185824.1:p.Arg393= NP_001185824.1:p.Arg393His
aminoacylase-1 isoform d NP_001185827.1:p.Arg358= NP_001185827.1:p.Arg358His
aminoacylase-1 isoform c NP_001185826.1:p.Arg328= NP_001185826.1:p.Arg328His
aminoacylase-1 isoform b NP_001185825.1:p.Arg321= NP_001185825.1:p.Arg321His
ABHD14A-ACY1 readthrough (NMD candidate) NP_001303260.1:p.Arg483= NP_001303260.1:p.Arg483His
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#.

57 SubSNP, 16 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss275513908 Nov 22, 2010 (133)
2 1000GENOMES ss330687245 May 09, 2011 (134)
3 NHLBI-ESP ss342133068 May 09, 2011 (134)
4 1000GENOMES ss489880404 May 04, 2012 (137)
5 EXOME_CHIP ss491340603 May 04, 2012 (137)
6 CLINSEQ_SNP ss491835320 May 04, 2012 (137)
7 ILLUMINA ss780817538 Sep 08, 2015 (146)
8 ILLUMINA ss783499823 Sep 08, 2015 (146)
9 EVA-GONL ss978578735 Aug 21, 2014 (142)
10 1000GENOMES ss1303958197 Aug 21, 2014 (142)
11 EVA_FINRISK ss1584027996 Apr 01, 2015 (144)
12 EVA_DECODE ss1588049694 Apr 01, 2015 (144)
13 EVA_UK10K_ALSPAC ss1607044216 Apr 01, 2015 (144)
14 EVA_UK10K_TWINSUK ss1650038249 Apr 01, 2015 (144)
15 EVA_EXAC ss1687036475 Apr 01, 2015 (144)
16 EVA_MGP ss1711018521 Apr 01, 2015 (144)
17 ILLUMINA ss1752474440 Sep 08, 2015 (146)
18 ILLUMINA ss1917767817 Feb 12, 2016 (147)
19 ILLUMINA ss1946083429 Feb 12, 2016 (147)
20 ILLUMINA ss1958563841 Feb 12, 2016 (147)
21 JJLAB ss2021468979 Sep 14, 2016 (149)
22 HUMAN_LONGEVITY ss2251484009 Dec 20, 2016 (150)
23 GNOMAD ss2733800033 Nov 08, 2017 (151)
24 GNOMAD ss2747021150 Nov 08, 2017 (151)
25 GNOMAD ss2792846039 Nov 08, 2017 (151)
26 AFFY ss2985257156 Nov 08, 2017 (151)
27 SWEGEN ss2992297560 Nov 08, 2017 (151)
28 ILLUMINA ss3022239798 Nov 08, 2017 (151)
29 ILLUMINA ss3628657784 Oct 12, 2018 (152)
30 ILLUMINA ss3634894877 Oct 12, 2018 (152)
31 ILLUMINA ss3640602178 Oct 12, 2018 (152)
32 ILLUMINA ss3644816003 Oct 12, 2018 (152)
33 ILLUMINA ss3652714125 Oct 12, 2018 (152)
34 ILLUMINA ss3654025541 Oct 12, 2018 (152)
35 EGCUT_WGS ss3660218669 Jul 13, 2019 (153)
36 EVA_DECODE ss3709209676 Jul 13, 2019 (153)
37 ILLUMINA ss3726015804 Jul 13, 2019 (153)
38 ACPOP ss3729876792 Jul 13, 2019 (153)
39 ILLUMINA ss3744510953 Jul 13, 2019 (153)
40 ILLUMINA ss3745194649 Jul 13, 2019 (153)
41 PAGE_CC ss3771031637 Jul 13, 2019 (153)
42 ILLUMINA ss3772690312 Jul 13, 2019 (153)
43 EVA ss3823919522 Apr 25, 2020 (154)
44 EVA ss3825634079 Apr 25, 2020 (154)
45 EVA ss3827803175 Apr 25, 2020 (154)
46 SGDP_PRJ ss3855822908 Apr 25, 2020 (154)
47 TOPMED ss4564329149 Apr 26, 2021 (155)
48 1000G_HIGH_COVERAGE ss5254049112 Oct 12, 2022 (156)
49 EVA ss5339740853 Oct 12, 2022 (156)
50 HUGCELL_USP ss5453442769 Oct 12, 2022 (156)
51 1000G_HIGH_COVERAGE ss5532397938 Oct 12, 2022 (156)
52 SANFORD_IMAGENETICS ss5632108823 Oct 12, 2022 (156)
53 EVA ss5800106771 Oct 12, 2022 (156)
54 EVA ss5825739788 Oct 12, 2022 (156)
55 EVA ss5847965193 Oct 12, 2022 (156)
56 EVA ss5868789402 Oct 12, 2022 (156)
57 EVA ss5960400635 Oct 12, 2022 (156)
58 1000Genomes NC_000003.11 - 52023042 Oct 12, 2018 (152)
59 1000Genomes_30x NC_000003.12 - 51989026 Oct 12, 2022 (156)
60 The Avon Longitudinal Study of Parents and Children NC_000003.11 - 52023042 Oct 12, 2018 (152)
61 Genetic variation in the Estonian population NC_000003.11 - 52023042 Oct 12, 2018 (152)
62 ExAC NC_000003.11 - 52023042 Oct 12, 2018 (152)
63 FINRISK NC_000003.11 - 52023042 Apr 25, 2020 (154)
64 gnomAD - Genomes NC_000003.12 - 51989026 Apr 26, 2021 (155)
65 gnomAD - Exomes NC_000003.11 - 52023042 Jul 13, 2019 (153)
66 Genome of the Netherlands Release 5 NC_000003.11 - 52023042 Apr 25, 2020 (154)
67 Medical Genome Project healthy controls from Spanish population NC_000003.11 - 52023042 Apr 25, 2020 (154)
68 Northern Sweden NC_000003.11 - 52023042 Jul 13, 2019 (153)
69 The PAGE Study NC_000003.12 - 51989026 Jul 13, 2019 (153)
70 SGDP_PRJ NC_000003.11 - 52023042 Apr 25, 2020 (154)
71 TopMed NC_000003.12 - 51989026 Apr 26, 2021 (155)
72 UK 10K study - Twins NC_000003.11 - 52023042 Oct 12, 2018 (152)
73 ALFA NC_000003.12 - 51989026 Apr 26, 2021 (155)
74 ClinVar RCV000019742.29 Oct 12, 2018 (152)
75 ClinVar RCV000292281.3 Oct 12, 2022 (156)
76 ClinVar RCV000488111.13 Oct 12, 2022 (156)
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
ss491835320, ss1588049694 NC_000003.10:51998081:G:A NC_000003.12:51989025:G:A (self)
15144699, 8421921, 5956917, 6962666, 24457, 2878827, 3693639, 135060, 3161657, 7839888, 8421921, ss330687245, ss342133068, ss489880404, ss491340603, ss780817538, ss783499823, ss978578735, ss1303958197, ss1584027996, ss1607044216, ss1650038249, ss1687036475, ss1711018521, ss1752474440, ss1917767817, ss1946083429, ss1958563841, ss2021468979, ss2733800033, ss2747021150, ss2792846039, ss2985257156, ss2992297560, ss3022239798, ss3628657784, ss3634894877, ss3640602178, ss3644816003, ss3652714125, ss3654025541, ss3660218669, ss3729876792, ss3744510953, ss3745194649, ss3772690312, ss3823919522, ss3825634079, ss3827803175, ss3855822908, ss5339740853, ss5632108823, ss5800106771, ss5825739788, ss5847965193, ss5960400635 NC_000003.11:52023041:G:A NC_000003.12:51989025:G:A (self)
RCV000019742.29, RCV000292281.3, RCV000488111.13, 19923873, 107516920, 253106, 401706704, 2250767336, ss275513908, ss2251484009, ss3709209676, ss3726015804, ss3771031637, ss4564329149, ss5254049112, ss5453442769, ss5532397938, ss5868789402 NC_000003.12:51989025:G:A NC_000003.12:51989025:G:A (self)
Help

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

2 citations for rs121912701
PMID Title Author Year Journal
17562838 Neurological findings in aminoacylase 1 deficiency. Sass JO et al. 2007 Neurology
21414403 The molecular basis of aminoacylase 1 deficiency. Sommer A et al. 2011 Biochimica et biophysica acta
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