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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 Aliases 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.

rs78778622

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr11:124660768 (GRCh38.p12) 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
T>A / T>C
Variation Type
SNV Single Nucleotide Variation
Frequency
C=0.0152 (1200/78696, PAGE_STUDY)
C=0.0410 (1288/31408, GnomAD)
C=0.0415 (540/13000, GO-ESP) (+ 5 more)
C=0.018 (89/5008, 1000G)
C=0.061 (274/4480, Estonian)
C=0.065 (249/3854, ALSPAC)
C=0.064 (238/3708, TWINSUK)
C=0.08 (46/600, NorthernSweden)
Clinical Significance
Reported in ClinVar
Gene : Consequence
SIAE : Missense Variant
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.p12 chr 11 NC_000011.10:g.124660768T>A
GRCh38.p12 chr 11 NC_000011.10:g.124660768T>C
GRCh37.p13 chr 11 NC_000011.9:g.124530664T>A
GRCh37.p13 chr 11 NC_000011.9:g.124530664T>C
SIAE RefSeqGene NG_028132.1:g.20536A>T
SIAE RefSeqGene NG_028132.1:g.20536A>G
Gene: SIAE, sialic acid acetylesterase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
SIAE transcript variant 2 NM_001199922.1:c.160A>T M [ATG] > L [TTG] Coding Sequence Variant
sialate O-acetylesterase isoform 2 NP_001186851.1:p.Met54Leu M (Met) > L (Leu) Missense Variant
SIAE transcript variant 2 NM_001199922.1:c.160A>G M [ATG] > V [GTG] Coding Sequence Variant
sialate O-acetylesterase isoform 2 NP_001186851.1:p.Met54Val M (Met) > V (Val) Missense Variant
SIAE transcript variant 1 NM_170601.5:c.265A>T M [ATG] > L [TTG] Coding Sequence Variant
sialate O-acetylesterase isoform 1 precursor NP_733746.1:p.Met89Leu M (Met) > L (Leu) Missense Variant
SIAE transcript variant 1 NM_170601.5:c.265A>G M [ATG] > V [GTG] Coding Sequence Variant
sialate O-acetylesterase isoform 1 precursor NP_733746.1:p.Met89Val M (Met) > V (Val) Missense Variant
SIAE transcript variant X1 XM_017017930.1:c. N/A 5 Prime UTR 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: C (allele ID: 16391 )
ClinVar Accession Disease Names Clinical Significance
RCV000001417.2 Autoimmune disease 6 Risk-Factor
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
The PAGE Study Global Study-wide 78696 T=0.9848 C=0.0152
The PAGE Study AfricanAmerican Sub 32514 T=0.9887 C=0.0113
The PAGE Study Mexican Sub 10808 T=0.9851 C=0.0149
The PAGE Study Asian Sub 8318 T=0.998 C=0.002
The PAGE Study PuertoRican Sub 7916 T=0.969 C=0.031
The PAGE Study NativeHawaiian Sub 4534 T=0.985 C=0.015
The PAGE Study Cuban Sub 4230 T=0.972 C=0.028
The PAGE Study Dominican Sub 3828 T=0.980 C=0.020
The PAGE Study CentralAmerican Sub 2450 T=0.983 C=0.017
The PAGE Study SouthAmerican Sub 1982 T=0.983 C=0.017
The PAGE Study NativeAmerican Sub 1260 T=0.963 C=0.037
The PAGE Study SouthAsian Sub 856 T=0.97 C=0.03
gnomAD - Genomes Global Study-wide 31408 T=0.9590 C=0.0410
gnomAD - Genomes European Sub 18912 T=0.9408 C=0.0592
gnomAD - Genomes African Sub 8712 T=0.990 C=0.010
gnomAD - Genomes East Asian Sub 1560 T=1.000 C=0.000
gnomAD - Genomes Other Sub 1086 T=0.947 C=0.053
gnomAD - Genomes American Sub 848 T=0.98 C=0.02
gnomAD - Genomes Ashkenazi Jewish Sub 290 T=0.98 C=0.02
GO Exome Sequencing Project Global Study-wide 13000 T=0.9585 C=0.0415
GO Exome Sequencing Project European American Sub 8598 T=0.943 C=0.057
GO Exome Sequencing Project African American Sub 4402 T=0.989 C=0.011
1000Genomes Global Study-wide 5008 T=0.982 C=0.018
1000Genomes African Sub 1322 T=1.000 C=0.000
1000Genomes East Asian Sub 1008 T=0.998 C=0.002
1000Genomes Europe Sub 1006 T=0.948 C=0.052
1000Genomes South Asian Sub 978 T=0.99 C=0.01
1000Genomes American Sub 694 T=0.97 C=0.03
Genetic variation in the Estonian population Estonian Study-wide 4480 T=0.939 C=0.061
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 T=0.935 C=0.065
UK 10K study - Twins TWIN COHORT Study-wide 3708 T=0.936 C=0.064
Northern Sweden ACPOP Study-wide 600 T=0.92 C=0.08
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 T= A C Note
GRCh38.p12 chr 11 NC_000011.10:g.12...

NC_000011.10:g.124660768=

NC_000011.10:g.12...

NC_000011.10:g.124660768T>A

NC_000011.10:g.12...

NC_000011.10:g.124660768T>C

GRCh37.p13 chr 11 NC_000011.9:g.124...

NC_000011.9:g.124530664=

NC_000011.9:g.124...

NC_000011.9:g.124530664T>A

NC_000011.9:g.124...

NC_000011.9:g.124530664T>C

SIAE RefSeqGene NG_028132.1:g.20536= NG_028132.1:g.205...

NG_028132.1:g.20536A>T

NG_028132.1:g.205...

NG_028132.1:g.20536A>G

SIAE transcript variant 1 NM_170601.4:c.265= NM_170601.4:c.265A>T NM_170601.4:c.265A>G
SIAE transcript variant 1 NM_170601.5:c.265= NM_170601.5:c.265A>T NM_170601.5:c.265A>G
SIAE transcript variant 2 NM_001199922.1:c....

NM_001199922.1:c.160=

NM_001199922.1:c....

NM_001199922.1:c.160A>T

NM_001199922.1:c....

NM_001199922.1:c.160A>G

SIAE transcript variant X1 XM_017017930.1:c....

XM_017017930.1:c.-2988=

XM_017017930.1:c....

XM_017017930.1:c.-2988A>T

XM_017017930.1:c....

XM_017017930.1:c.-2988A>G

sialate O-acetylesterase isoform 1 precursor NP_733746.1:p.Met89= NP_733746.1:p.Met...

NP_733746.1:p.Met89Leu

NP_733746.1:p.Met...

NP_733746.1:p.Met89Val

sialate O-acetylesterase isoform 2 NP_001186851.1:p....

NP_001186851.1:p.Met54=

NP_001186851.1:p....

NP_001186851.1:p.Met54Leu

NP_001186851.1:p....

NP_001186851.1:p.Met54Val

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#.

72 SubSNP, 12 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 ILLUMINA ss161037993 Dec 01, 2009 (131)
2 COMPLETE_GENOMICS ss175306162 Jul 04, 2010 (132)
3 1000GENOMES ss235756862 Jul 15, 2010 (132)
4 1000GENOMES ss242349363 Jul 15, 2010 (132)
5 GMI ss286475445 Apr 25, 2013 (138)
6 NHLBI-ESP ss342344387 May 09, 2011 (134)
7 ILLUMINA ss479463385 Sep 08, 2015 (146)
8 ILLUMINA ss482751436 May 04, 2012 (137)
9 ILLUMINA ss484343891 May 04, 2012 (137)
10 1000GENOMES ss491032157 May 04, 2012 (137)
11 EXOME_CHIP ss491461216 May 04, 2012 (137)
12 CLINSEQ_SNP ss491656424 May 04, 2012 (137)
13 ILLUMINA ss536526770 Sep 08, 2015 (146)
14 NCBI-CURATED-RECORDS ss537713589 Jan 04, 2013 (137)
15 ILLUMINA ss779532387 Sep 08, 2015 (146)
16 ILLUMINA ss780905685 Aug 21, 2014 (142)
17 ILLUMINA ss782618191 Sep 08, 2015 (146)
18 ILLUMINA ss783593012 Aug 21, 2014 (142)
19 ILLUMINA ss835002964 Sep 08, 2015 (146)
20 EVA-GONL ss989062803 Aug 21, 2014 (142)
21 JMKIDD_LAB ss1067529478 Aug 21, 2014 (142)
22 JMKIDD_LAB ss1078120628 Aug 21, 2014 (142)
23 1000GENOMES ss1343349725 Aug 21, 2014 (142)
24 EVA_GENOME_DK ss1576012277 Apr 01, 2015 (144)
25 EVA_FINRISK ss1584078917 Apr 01, 2015 (144)
26 EVA_DECODE ss1598731518 Apr 01, 2015 (144)
27 EVA_UK10K_ALSPAC ss1627671620 Apr 01, 2015 (144)
28 EVA_UK10K_TWINSUK ss1670665653 Apr 01, 2015 (144)
29 EVA_EXAC ss1690693792 Apr 01, 2015 (144)
30 EVA_EXAC ss1690693793 Apr 01, 2015 (144)
31 EVA_MGP ss1711313112 Apr 01, 2015 (144)
32 ILLUMINA ss1752001172 Sep 08, 2015 (146)
33 ILLUMINA ss1917868230 Feb 12, 2016 (147)
34 WEILL_CORNELL_DGM ss1932425932 Feb 12, 2016 (147)
35 ILLUMINA ss1946326142 Feb 12, 2016 (147)
36 ILLUMINA ss1959396193 Feb 12, 2016 (147)
37 JJLAB ss2026958380 Sep 14, 2016 (149)
38 ILLUMINA ss2094869470 Dec 20, 2016 (150)
39 ILLUMINA ss2095028160 Dec 20, 2016 (150)
40 USC_VALOUEV ss2155274697 Dec 20, 2016 (150)
41 HUMAN_LONGEVITY ss2186497455 Dec 20, 2016 (150)
42 TOPMED ss2350091577 Dec 20, 2016 (150)
43 ILLUMINA ss2632900961 Nov 08, 2017 (151)
44 GNOMAD ss2739482759 Nov 08, 2017 (151)
45 GNOMAD ss2748767773 Nov 08, 2017 (151)
46 GNOMAD ss2905526921 Nov 08, 2017 (151)
47 AFFY ss2984961027 Nov 08, 2017 (151)
48 SWEGEN ss3008934670 Nov 08, 2017 (151)
49 ILLUMINA ss3021387310 Nov 08, 2017 (151)
50 TOPMED ss3158842346 Nov 08, 2017 (151)
51 CSHL ss3349840520 Nov 08, 2017 (151)
52 ILLUMINA ss3626773883 Oct 12, 2018 (152)
53 ILLUMINA ss3626773884 Oct 12, 2018 (152)
54 ILLUMINA ss3630914006 Oct 12, 2018 (152)
55 ILLUMINA ss3634481298 Oct 12, 2018 (152)
56 ILLUMINA ss3636165322 Oct 12, 2018 (152)
57 ILLUMINA ss3640188632 Oct 12, 2018 (152)
58 ILLUMINA ss3644579030 Oct 12, 2018 (152)
59 BIOINF_KMB_FNS_UNIBA ss3645226230 Oct 12, 2018 (152)
60 OMUKHERJEE_ADBS ss3646434429 Oct 12, 2018 (152)
61 ILLUMINA ss3651756726 Oct 12, 2018 (152)
62 ILLUMINA ss3651756727 Oct 12, 2018 (152)
63 ILLUMINA ss3653733339 Oct 12, 2018 (152)
64 EGCUT_WGS ss3676264544 Jul 13, 2019 (153)
65 EVA_DECODE ss3692788853 Jul 13, 2019 (153)
66 ILLUMINA ss3725286533 Jul 13, 2019 (153)
67 ACPOP ss3738624257 Jul 13, 2019 (153)
68 ILLUMINA ss3744389371 Jul 13, 2019 (153)
69 ILLUMINA ss3744782049 Jul 13, 2019 (153)
70 EVA ss3749933146 Jul 13, 2019 (153)
71 PAGE_CC ss3771660865 Jul 13, 2019 (153)
72 ILLUMINA ss3772281750 Jul 13, 2019 (153)
73 1000Genomes NC_000011.9 - 124530664 Oct 12, 2018 (152)
74 The Avon Longitudinal Study of Parents and Children NC_000011.9 - 124530664 Oct 12, 2018 (152)
75 Genetic variation in the Estonian population NC_000011.9 - 124530664 Oct 12, 2018 (152)
76 ExAC

Submission ignored due to conflicting rows:
Row 974101 (NC_000011.9:124530663:T:T 116644/121342, NC_000011.9:124530663:T:C 4698/121342)
Row 974102 (NC_000011.9:124530663:T:T 121341/121342, NC_000011.9:124530663:T:A 1/121342)

- Oct 12, 2018 (152)
77 ExAC

Submission ignored due to conflicting rows:
Row 974101 (NC_000011.9:124530663:T:T 116644/121342, NC_000011.9:124530663:T:C 4698/121342)
Row 974102 (NC_000011.9:124530663:T:T 121341/121342, NC_000011.9:124530663:T:A 1/121342)

- Oct 12, 2018 (152)
78 gnomAD - Genomes NC_000011.9 - 124530664 Jul 13, 2019 (153)
79 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 8704803 (NC_000011.9:124530663:T:T 251409/251410, NC_000011.9:124530663:T:A 1/251410)
Row 8704804 (NC_000011.9:124530663:T:T 241932/251410, NC_000011.9:124530663:T:C 9478/251410)

- Jul 13, 2019 (153)
80 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 8704803 (NC_000011.9:124530663:T:T 251409/251410, NC_000011.9:124530663:T:A 1/251410)
Row 8704804 (NC_000011.9:124530663:T:T 241932/251410, NC_000011.9:124530663:T:C 9478/251410)

- Jul 13, 2019 (153)
81 GO Exome Sequencing Project NC_000011.9 - 124530664 Oct 12, 2018 (152)
82 Northern Sweden NC_000011.9 - 124530664 Jul 13, 2019 (153)
83 The PAGE Study NC_000011.10 - 124660768 Jul 13, 2019 (153)
84 UK 10K study - Twins NC_000011.9 - 124530664 Oct 12, 2018 (152)
85 ClinVar RCV000001417.2 Oct 12, 2018 (152)
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
ss1690693793, ss2739482759 NC_000011.9:124530663:T:A NC_000011.10:124660767:T:A (self)
ss175306162, ss286475445, ss482751436, ss491656424, ss1598731518, ss2094869470 NC_000011.8:124035873:T:C NC_000011.10:124660767:T:C (self)
55945715, 31061579, 22002792, 152748309, 1142048, 11909122, 31061579, ss235756862, ss242349363, ss342344387, ss479463385, ss484343891, ss491032157, ss491461216, ss536526770, ss779532387, ss780905685, ss782618191, ss783593012, ss835002964, ss989062803, ss1067529478, ss1078120628, ss1343349725, ss1576012277, ss1584078917, ss1627671620, ss1670665653, ss1690693792, ss1711313112, ss1752001172, ss1917868230, ss1932425932, ss1946326142, ss1959396193, ss2026958380, ss2095028160, ss2155274697, ss2350091577, ss2632900961, ss2739482759, ss2748767773, ss2905526921, ss2984961027, ss3008934670, ss3021387310, ss3349840520, ss3626773883, ss3626773884, ss3630914006, ss3634481298, ss3636165322, ss3640188632, ss3644579030, ss3646434429, ss3651756726, ss3651756727, ss3653733339, ss3676264544, ss3738624257, ss3744389371, ss3744782049, ss3749933146, ss3772281750 NC_000011.9:124530663:T:C NC_000011.10:124660767:T:C (self)
RCV000001417.2, 882334, ss537713589, ss2186497455, ss3158842346, ss3645226230, ss3692788853, ss3725286533, ss3771660865 NC_000011.10:124660767:T:C NC_000011.10:124660767:T:C (self)
ss161037993 NT_033899.8:28093079:T:C NC_000011.10:124660767:T:C (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 rs78778622
PMID Title Author Year Journal
20555325 Functionally defective germline variants of sialic acid acetylesterase in autoimmunity. Surolia I et al. 2010 Nature

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.post308+0fe9b3b