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dbSNP Short Genetic Variations

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.

rs185919705

Current Build 155

Released April 9, 2021

Organism
Homo sapiens
Position
chr15:86674435 (GRCh38.p13) 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
C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.002233 (591/264690, TOPMED)
T=0.001790 (440/245850, GnomAD_exome)
T=0.002783 (567/203738, ALFA) (+ 11 more)
T=0.001997 (280/140242, GnomAD)
T=0.001751 (204/116480, ExAC)
T=0.00142 (112/78698, PAGE_STUDY)
T=0.00012 (2/16760, 8.3KJPN)
T=0.00262 (32/12192, GO-ESP)
T=0.0016 (8/5008, 1000G)
T=0.0002 (1/4480, Estonian)
T=0.0021 (8/3854, ALSPAC)
T=0.0016 (6/3708, TWINSUK)
T=0.004 (4/998, GoNL)
T=0.002 (1/534, MGP)
Clinical Significance
Reported in ClinVar
Gene : Consequence
AGBL1 : Stop Gained
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.p13 chr 15 NC_000015.10:g.86674435C>T
GRCh37.p13 chr 15 NC_000015.9:g.87217666C>T
AGBL1 RefSeqGene NG_033836.2:g.599628C>T
Gene: AGBL1, AGBL carboxypeptidase 1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
AGBL1 transcript variant 2 NM_152336.4:c.3220C>T R [CGA] > * [TGA] Coding Sequence Variant
cytosolic carboxypeptidase 4 isoform 2 NP_689549.3:p.Arg1074Ter R (Arg) > * (Ter) Stop Gained
AGBL1 transcript variant 1 NM_001386094.1:c.3157C>T R [CGG] > W [TGG] Coding Sequence Variant
cytosolic carboxypeptidase 4 isoform 1 NP_001373023.1:p.Arg1053T…

NP_001373023.1:p.Arg1053Trp

R (Arg) > W (Trp) Missense Variant
AGBL1 transcript variant X6 XM_011521228.3:c. N/A Genic Downstream Transcript Variant
AGBL1 transcript variant X10 XM_011521230.3:c. N/A Genic Downstream Transcript Variant
AGBL1 transcript variant X5 XM_017021920.2:c. N/A Genic Downstream Transcript Variant
AGBL1 transcript variant X8 XM_017021921.2:c. N/A Genic Downstream Transcript Variant
AGBL1 transcript variant X2 XM_017021918.2:c.3124C>T R [CGG] > W [TGG] Coding Sequence Variant
cytosolic carboxypeptidase 4 isoform X2 XP_016877407.1:p.Arg1042T…

XP_016877407.1:p.Arg1042Trp

R (Arg) > W (Trp) Missense Variant
AGBL1 transcript variant X3 XM_017021919.2:c.3073C>T R [CGG] > W [TGG] Coding Sequence Variant
cytosolic carboxypeptidase 4 isoform X3 XP_016877408.1:p.Arg1025T…

XP_016877408.1:p.Arg1025Trp

R (Arg) > W (Trp) Missense Variant
AGBL1 transcript variant X4 XM_011521227.3:c.3157C>T R [CGA] > * [TGA] Coding Sequence Variant
cytosolic carboxypeptidase 4 isoform X4 XP_011519529.1:p.Arg1053T…

XP_011519529.1:p.Arg1053Ter

R (Arg) > * (Ter) Stop Gained
AGBL1 transcript variant X7 XR_931750.3:n. N/A Genic Downstream Transcript Variant
AGBL1 transcript variant X9 XR_931751.3: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.

Allele: T (allele ID: 94338 )
ClinVar Accession Disease Names Clinical Significance
RCV000074408.4 Corneal dystrophy, Fuchs endothelial, 8 Pathogenic

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: 20201027095038
Population Group Sample Size Ref Allele Alt Allele
Total Global 203738 C=0.997217 T=0.002783
European Sub 174396 C=0.997013 T=0.002987
African Sub 4952 C=0.9986 T=0.0014
African Others Sub 176 C=1.000 T=0.000
African American Sub 4776 C=0.9985 T=0.0015
Asian Sub 6348 C=1.0000 T=0.0000
East Asian Sub 4500 C=1.0000 T=0.0000
Other Asian Sub 1848 C=1.0000 T=0.0000
Latin American 1 Sub 796 C=0.999 T=0.001
Latin American 2 Sub 968 C=0.998 T=0.002
South Asian Sub 280 C=1.000 T=0.000
Other Sub 15998 C=0.99775 T=0.00225


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 C=0.997767 T=0.002233
gnomAD - Exomes Global Study-wide 245850 C=0.998210 T=0.001790
gnomAD - Exomes European Sub 132290 C=0.997815 T=0.002185
gnomAD - Exomes Asian Sub 48156 C=0.99994 T=0.00006
gnomAD - Exomes American Sub 34252 C=0.99886 T=0.00114
gnomAD - Exomes African Sub 15304 C=0.99954 T=0.00046
gnomAD - Exomes Ashkenazi Jewish Sub 9898 C=0.9910 T=0.0090
gnomAD - Exomes Other Sub 5950 C=0.9978 T=0.0022
gnomAD - Genomes Global Study-wide 140242 C=0.998003 T=0.001997
gnomAD - Genomes European Sub 75954 C=0.99759 T=0.00241
gnomAD - Genomes African Sub 42026 C=0.99960 T=0.00040
gnomAD - Genomes American Sub 13652 C=0.99656 T=0.00344
gnomAD - Genomes Ashkenazi Jewish Sub 3324 C=0.9913 T=0.0087
gnomAD - Genomes East Asian Sub 3132 C=0.9997 T=0.0003
gnomAD - Genomes Other Sub 2154 C=0.9986 T=0.0014
ExAC Global Study-wide 116480 C=0.998249 T=0.001751
ExAC Europe Sub 71512 C=0.99739 T=0.00261
ExAC Asian Sub 23738 C=0.99983 T=0.00017
ExAC American Sub 11252 C=0.99920 T=0.00080
ExAC African Sub 9126 C=0.9996 T=0.0004
ExAC Other Sub 852 C=1.000 T=0.000
The PAGE Study Global Study-wide 78698 C=0.99858 T=0.00142
The PAGE Study AfricanAmerican Sub 32514 C=0.99911 T=0.00089
The PAGE Study Mexican Sub 10810 C=0.99889 T=0.00111
The PAGE Study Asian Sub 8318 C=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 C=0.9951 T=0.0049
The PAGE Study NativeHawaiian Sub 4534 C=0.9989 T=0.0011
The PAGE Study Cuban Sub 4230 C=0.9962 T=0.0038
The PAGE Study Dominican Sub 3826 C=0.9995 T=0.0005
The PAGE Study CentralAmerican Sub 2450 C=0.9988 T=0.0012
The PAGE Study SouthAmerican Sub 1982 C=0.9985 T=0.0015
The PAGE Study NativeAmerican Sub 1260 C=0.9976 T=0.0024
The PAGE Study SouthAsian Sub 856 C=1.000 T=0.000
8.3KJPN JAPANESE Study-wide 16760 C=0.99988 T=0.00012
GO Exome Sequencing Project Global Study-wide 12192 C=0.99738 T=0.00262
GO Exome Sequencing Project European American Sub 8280 C=0.9965 T=0.0035
GO Exome Sequencing Project African American Sub 3912 C=0.9992 T=0.0008
1000Genomes Global Study-wide 5008 C=0.9984 T=0.0016
1000Genomes African Sub 1322 C=1.0000 T=0.0000
1000Genomes East Asian Sub 1008 C=1.0000 T=0.0000
1000Genomes Europe Sub 1006 C=0.9950 T=0.0050
1000Genomes South Asian Sub 978 C=0.999 T=0.001
1000Genomes American Sub 694 C=0.997 T=0.003
Genetic variation in the Estonian population Estonian Study-wide 4480 C=0.9998 T=0.0002
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=0.9979 T=0.0021
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=0.9984 T=0.0016
Genome of the Netherlands Release 5 Genome of the Netherlands Study-wide 998 C=0.996 T=0.004
Medical Genome Project healthy controls from Spanish population Spanish controls Study-wide 534 C=0.998 T=0.002
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 C= T
GRCh38.p13 chr 15 NC_000015.10:g.86674435= NC_000015.10:g.86674435C>T
GRCh37.p13 chr 15 NC_000015.9:g.87217666= NC_000015.9:g.87217666C>T
AGBL1 RefSeqGene NG_033836.2:g.599628= NG_033836.2:g.599628C>T
AGBL1 transcript variant 2 NM_152336.4:c.3220= NM_152336.4:c.3220C>T
AGBL1 transcript NM_152336.3:c.3220= NM_152336.3:c.3220C>T
AGBL1 transcript NM_152336.2:c.3082= NM_152336.2:c.3082C>T
AGBL1 transcript variant 1 NM_001386094.1:c.3157= NM_001386094.1:c.3157C>T
AGBL1 transcript variant X4 XM_011521227.3:c.3157= XM_011521227.3:c.3157C>T
AGBL1 transcript variant X2 XM_017021918.2:c.3124= XM_017021918.2:c.3124C>T
AGBL1 transcript variant X3 XM_017021919.2:c.3073= XM_017021919.2:c.3073C>T
cytosolic carboxypeptidase 4 isoform 2 NP_689549.3:p.Arg1074= NP_689549.3:p.Arg1074Ter
cytosolic carboxypeptidase 4 isoform 1 NP_001373023.1:p.Arg1053= NP_001373023.1:p.Arg1053Trp
cytosolic carboxypeptidase 4 isoform X4 XP_011519529.1:p.Arg1053= XP_011519529.1:p.Arg1053Ter
cytosolic carboxypeptidase 4 isoform X2 XP_016877407.1:p.Arg1042= XP_016877407.1:p.Arg1042Trp
cytosolic carboxypeptidase 4 isoform X3 XP_016877408.1:p.Arg1025= XP_016877408.1:p.Arg1025Trp
cytosolic carboxypeptidase 4 NP_689549.2:p.Arg1028= NP_689549.2:p.Arg1028Ter
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#.

44 SubSNP, 14 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss464322032 Sep 17, 2011 (135)
2 EXOME_CHIP ss491498944 May 04, 2012 (137)
3 CLINSEQ_SNP ss491706632 May 04, 2012 (137)
4 NHLBI-ESP ss713252651 Apr 25, 2013 (138)
5 ILLUMINA ss780712116 Sep 08, 2015 (146)
6 ILLUMINA ss783387001 Sep 08, 2015 (146)
7 OMIM-CURATED-RECORDS ss902923715 Dec 03, 2013 (138)
8 EVA-GONL ss992040956 Aug 21, 2014 (142)
9 1000GENOMES ss1354453128 Aug 21, 2014 (142)
10 EVA_UK10K_ALSPAC ss1633527177 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1676521210 Apr 01, 2015 (144)
12 EVA_EXAC ss1691978751 Apr 01, 2015 (144)
13 EVA_DECODE ss1696068114 Apr 01, 2015 (144)
14 EVA_MGP ss1711408515 Apr 01, 2015 (144)
15 ILLUMINA ss1752175313 Sep 08, 2015 (146)
16 ILLUMINA ss1917900232 Feb 12, 2016 (147)
17 ILLUMINA ss1946401151 Feb 12, 2016 (147)
18 ILLUMINA ss1959633774 Feb 12, 2016 (147)
19 HUMAN_LONGEVITY ss2208780860 Dec 20, 2016 (150)
20 TOPMED ss2373321181 Dec 20, 2016 (150)
21 GNOMAD ss2749377079 Nov 08, 2017 (151)
22 GNOMAD ss2937759553 Nov 08, 2017 (151)
23 AFFY ss2985050091 Nov 08, 2017 (151)
24 ILLUMINA ss3021657218 Nov 08, 2017 (151)
25 TOPMED ss3234215266 Nov 08, 2017 (151)
26 ILLUMINA ss3627420185 Oct 12, 2018 (152)
27 ILLUMINA ss3634618964 Oct 12, 2018 (152)
28 ILLUMINA ss3640326284 Oct 12, 2018 (152)
29 ILLUMINA ss3644654257 Oct 12, 2018 (152)
30 ILLUMINA ss3652059810 Oct 12, 2018 (152)
31 ILLUMINA ss3653822012 Oct 12, 2018 (152)
32 EGCUT_WGS ss3680819420 Jul 13, 2019 (153)
33 EVA_DECODE ss3698381398 Jul 13, 2019 (153)
34 ILLUMINA ss3725521247 Jul 13, 2019 (153)
35 ILLUMINA ss3744424293 Jul 13, 2019 (153)
36 ILLUMINA ss3744919495 Jul 13, 2019 (153)
37 PAGE_CC ss3771847350 Jul 13, 2019 (153)
38 ILLUMINA ss3772418001 Jul 13, 2019 (153)
39 EVA ss3824950198 Apr 27, 2020 (154)
40 EVA ss3825865474 Apr 27, 2020 (154)
41 EVA ss3834356321 Apr 27, 2020 (154)
42 EVA ss3986660992 Apr 27, 2021 (155)
43 TOPMED ss5000104343 Apr 27, 2021 (155)
44 TOMMO_GENOMICS ss5217366980 Apr 27, 2021 (155)
45 1000Genomes NC_000015.9 - 87217666 Oct 12, 2018 (152)
46 The Avon Longitudinal Study of Parents and Children NC_000015.9 - 87217666 Oct 12, 2018 (152)
47 Genetic variation in the Estonian population NC_000015.9 - 87217666 Oct 12, 2018 (152)
48 ExAC NC_000015.9 - 87217666 Oct 12, 2018 (152)
49 gnomAD - Genomes NC_000015.10 - 86674435 Apr 27, 2021 (155)
50 gnomAD - Exomes NC_000015.9 - 87217666 Jul 13, 2019 (153)
51 GO Exome Sequencing Project NC_000015.9 - 87217666 Oct 12, 2018 (152)
52 Genome of the Netherlands Release 5 NC_000015.9 - 87217666 Apr 27, 2020 (154)
53 Medical Genome Project healthy controls from Spanish population NC_000015.9 - 87217666 Apr 27, 2020 (154)
54 The PAGE Study NC_000015.10 - 86674435 Jul 13, 2019 (153)
55 8.3KJPN NC_000015.9 - 87217666 Apr 27, 2021 (155)
56 TopMed NC_000015.10 - 86674435 Apr 27, 2021 (155)
57 UK 10K study - Twins NC_000015.9 - 87217666 Oct 12, 2018 (152)
58 ALFA NC_000015.10 - 86674435 Apr 27, 2021 (155)
59 ClinVar RCV000074408.4 Apr 27, 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
ss491706632, ss1696068114 NC_000015.8:85018669:C:T NC_000015.10:86674434:C:T (self)
67560317, 37519292, 26557668, 2363648, 10751052, 1407441, 16741488, 524275, 75336287, 37519292, ss464322032, ss491498944, ss713252651, ss780712116, ss783387001, ss992040956, ss1354453128, ss1633527177, ss1676521210, ss1691978751, ss1711408515, ss1752175313, ss1917900232, ss1946401151, ss1959633774, ss2373321181, ss2749377079, ss2937759553, ss2985050091, ss3021657218, ss3627420185, ss3634618964, ss3640326284, ss3644654257, ss3652059810, ss3653822012, ss3680819420, ss3744424293, ss3744919495, ss3772418001, ss3824950198, ss3825865474, ss3834356321, ss3986660992, ss5217366980 NC_000015.9:87217665:C:T NC_000015.10:86674434:C:T (self)
RCV000074408.4, 476353375, 1068819, 134849953, 215650003, 8103773362, ss902923715, ss2208780860, ss3234215266, ss3698381398, ss3725521247, ss3771847350, ss5000104343 NC_000015.10:86674434:C:T NC_000015.10:86674434:C:T (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 rs185919705
PMID Title Author Year Journal
24094747 Mutations in AGBL1 cause dominant late-onset Fuchs corneal dystrophy and alter protein-protein interaction with TCF4. Riazuddin SA et al. 2013 American journal of human genetics
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.post596+ae089ad