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dbSNP Short Genetic Variations

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.

rs145236923

Current Build 152

Released October 2, 2018

Organism
Homo sapiens
Position
chr9:98831947 (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
G>A
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.00125 (306/245556, GnomAD)
A=0.00159 (200/125568, TOPMED)
A=0.00123 (138/111936, ExAC) (+ 6 more)
A=0.0012 (38/30970, GnomAD)
A=0.0009 (12/13006, GO-ESP)
A=0.001 (4/5008, 1000G)
A=0.001 (5/4480, Estonian)
A=0.002 (9/3854, ALSPAC)
A=0.003 (11/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
GALNT12 : 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 9 NC_000009.12:g.98831947G>A
GRCh37.p13 chr 9 NC_000009.11:g.101594229G>A
GALNT12 RefSeqGene NG_028218.1:g.29249G>A
Gene: GALNT12, polypeptide N-acetylgalactosaminyltransferase 12 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GALNT12 transcript NM_024642.4:c.907G>A D [GAT] > N [AAT] Coding Sequence Variant
polypeptide N-acetylgalactosaminyltransferase 12 NP_078918.3:p.Asp303Asn D (Asp) > N (Asn) Missense Variant
GALNT12 transcript variant X5 XM_024447673.1:c. N/A 5 Prime UTR Variant
GALNT12 transcript variant X4 XM_006717287.1:c.16G>A D [GAT] > N [AAT] Coding Sequence Variant
polypeptide N-acetylgalactosaminyltransferase 12 isoform X4 XP_006717350.1:p.Asp6Asn D (Asp) > N (Asn) Missense Variant
GALNT12 transcript variant X3 XM_011519020.1:c.199G>A D [GAT] > N [AAT] Coding Sequence Variant
polypeptide N-acetylgalactosaminyltransferase 12 isoform X3 XP_011517322.1:p.Asp67Asn D (Asp) > N (Asn) Missense Variant
GALNT12 transcript variant X2 XM_017015133.1:c.655G>A D [GAT] > N [AAT] Coding Sequence Variant
polypeptide N-acetylgalactosaminyltransferase 12 isoform X2 XP_016870622.1:p.Asp219Asn D (Asp) > N (Asn) Missense Variant
GALNT12 transcript variant X1 XM_011519018.3:c.685G>A D [GAT] > N [AAT] Coding Sequence Variant
polypeptide N-acetylgalactosaminyltransferase 12 isoform X1 XP_011517320.1:p.Asp229Asn D (Asp) > N (Asn) 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: 226331 )
ClinVar Accession Disease Names Clinical Significance
RCV000210098.1 Hereditary cancer-predisposing syndrome Uncertain-Significance
RCV000229689.2 not specified Likely-Benign
RCV000656380.1 Adenomatous polyposis coli, attenuated Benign
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").

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Study Population Group Sample Size Ref Allele Alt Allele
gnomAD - Exomes Global Study-wide 245556 G=0.99875 A=0.00125
gnomAD - Exomes European Sub 133598 G=0.99821 A=0.00179
gnomAD - Exomes Asian Sub 47876 G=0.9999 A=0.0001
gnomAD - Exomes American Sub 33546 G=0.9990 A=0.0010
gnomAD - Exomes African Sub 15232 G=0.9995 A=0.0005
gnomAD - Exomes Ashkenazi Jewish Sub 9838 G=0.998 A=0.002
gnomAD - Exomes Other Sub 5466 G=0.999 A=0.001
TopMed Global Study-wide 125568 G=0.99841 A=0.00159
ExAC Global Study-wide 111936 G=0.99877 A=0.00123
ExAC Europe Sub 67848 G=0.9981 A=0.0019
ExAC Asian Sub 23150 G=1.0000 A=0.0000
ExAC American Sub 10692 G=0.9993 A=0.0007
ExAC African Sub 9398 G=1.000 A=0.000
ExAC Other Sub 848 G=1.00 A=0.00
gnomAD - Genomes Global Study-wide 30970 G=0.9988 A=0.0012
gnomAD - Genomes European Sub 18500 G=0.9984 A=0.0016
gnomAD - Genomes African Sub 8728 G=1.000 A=0.000
gnomAD - Genomes East Asian Sub 1622 G=0.999 A=0.001
gnomAD - Genomes Other Sub 982 G=1.00 A=0.00
gnomAD - Genomes American Sub 838 G=1.00 A=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 300 G=1.00 A=0.00
GO Exome Sequencing Project Global Study-wide 13006 G=0.9991 A=0.0009
GO Exome Sequencing Project European American Sub 8600 G=0.999 A=0.001
GO Exome Sequencing Project African American Sub 4406 G=1.000 A=0.000
1000Genomes Global Study-wide 5008 G=0.999 A=0.001
1000Genomes African Sub 1322 G=1.000 A=0.000
1000Genomes East Asian Sub 1008 G=1.000 A=0.000
1000Genomes Europe Sub 1006 G=0.997 A=0.003
1000Genomes South Asian Sub 978 G=1.00 A=0.00
1000Genomes American Sub 694 G=1.00 A=0.00
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.999 A=0.001
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 G=0.998 A=0.002
UK 10K study - Twins TWIN COHORT Study-wide 3708 G=0.997 A=0.003
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 Note
GRCh38.p12 chr 9 NC_000009.12:g.98831947G= NC_000009.12:g.98831947G>A
GRCh37.p13 chr 9 NC_000009.11:g.101594229G= NC_000009.11:g.10159422...

NC_000009.11:g.101594229G>A

GALNT12 RefSeqGene NG_028218.1:g.29249G= NG_028218.1:g.29249G>A
GALNT12 transcript NM_024642.4:c.907G= NM_024642.4:c.907G>A
GALNT12 transcript variant X1 XM_011519018.3:c.685G= XM_011519018.3:c.685G>A
GALNT12 transcript variant X5 XM_024447673.1:c.-1497G= XM_024447673.1:c.-1497G>A
GALNT12 transcript variant X3 XM_011519020.1:c.199G= XM_011519020.1:c.199G>A
GALNT12 transcript variant X4 XM_006717287.1:c.16G= XM_006717287.1:c.16G>A
GALNT12 transcript variant X2 XM_017015133.1:c.655G= XM_017015133.1:c.655G>A
polypeptide N-acetylgalactosaminyltransferase 12 NP_078918.3:p.Asp303= NP_078918.3:p.Asp303Asn
polypeptide N-acetylgalactosaminyltransferase 12 isoform X1 XP_011517320.1:p.Asp229= XP_011517320.1:p.Asp229Asn
polypeptide N-acetylgalactosaminyltransferase 12 isoform X3 XP_011517322.1:p.Asp67= XP_011517322.1:p.Asp67Asn
polypeptide N-acetylgalactosaminyltransferase 12 isoform X4 XP_006717350.1:p.Asp6= XP_006717350.1:p.Asp6Asn
polypeptide N-acetylgalactosaminyltransferase 12 isoform X2 XP_016870622.1:p.Asp219= XP_016870622.1:p.Asp219Asn
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#.

33 SubSNP, 9 Frequency, 3 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss335691697 May 09, 2011 (134)
2 NHLBI-ESP ss342278397 May 09, 2011 (134)
3 1000GENOMES ss490981426 May 04, 2012 (137)
4 EXOME_CHIP ss491425306 May 04, 2012 (137)
5 CLINSEQ_SNP ss491939749 May 04, 2012 (137)
6 ILLUMINA ss780878739 Sep 08, 2015 (146)
7 ILLUMINA ss783564313 Sep 08, 2015 (146)
8 EVA-GONL ss986791826 Aug 21, 2014 (142)
9 1000GENOMES ss1334752829 Aug 21, 2014 (142)
10 EVA_UK10K_ALSPAC ss1623183991 Apr 01, 2015 (144)
11 EVA_UK10K_TWINSUK ss1666178024 Apr 01, 2015 (144)
12 EVA_EXAC ss1689576516 Apr 01, 2015 (144)
13 EVA_MGP ss1711231233 Apr 01, 2015 (144)
14 ILLUMINA ss1752749356 Sep 08, 2015 (146)
15 ILLUMINA ss1917838468 Feb 12, 2016 (147)
16 ILLUMINA ss1946263713 Feb 12, 2016 (147)
17 ILLUMINA ss1959200217 Feb 12, 2016 (147)
18 HUMAN_LONGEVITY ss2312970171 Dec 20, 2016 (150)
19 TOPMED ss2483447327 Dec 20, 2016 (150)
20 GNOMAD ss2737747992 Nov 08, 2017 (151)
21 GNOMAD ss2748230602 Nov 08, 2017 (151)
22 GNOMAD ss2881227250 Nov 08, 2017 (151)
23 AFFY ss2985467837 Nov 08, 2017 (151)
24 SWEGEN ss3005305323 Nov 08, 2017 (151)
25 ILLUMINA ss3022947471 Nov 08, 2017 (151)
26 TOPMED ss3596040101 Nov 08, 2017 (151)
27 ILLUMINA ss3625987685 Oct 12, 2018 (152)
28 ILLUMINA ss3630313875 Oct 12, 2018 (152)
29 ILLUMINA ss3635223577 Oct 12, 2018 (152)
30 ILLUMINA ss3640930868 Oct 12, 2018 (152)
31 ILLUMINA ss3644997041 Oct 12, 2018 (152)
32 ILLUMINA ss3653500964 Oct 12, 2018 (152)
33 ILLUMINA ss3654232652 Oct 12, 2018 (152)
34 1000Genomes NC_000009.11 - 101594229 Oct 12, 2018 (152)
35 The Avon Longitudinal Study of Parents and Children NC_000009.11 - 101594229 Oct 12, 2018 (152)
36 Genetic variation in the Estonian population NC_000009.11 - 101594229 Oct 12, 2018 (152)
37 ExAC NC_000009.11 - 101594229 Oct 12, 2018 (152)
38 gnomAD - Genomes NC_000009.11 - 101594229 Oct 12, 2018 (152)
39 gnomAD - Exomes NC_000009.11 - 101594229 Oct 12, 2018 (152)
40 GO Exome Sequencing Project NC_000009.11 - 101594229 Oct 12, 2018 (152)
41 TopMed NC_000009.12 - 98831947 Oct 12, 2018 (152)
42 UK 10K study - Twins NC_000009.11 - 101594229 Oct 12, 2018 (152)
43 ClinVar RCV000210098.1 Oct 12, 2018 (152)
44 ClinVar RCV000229689.2 Oct 12, 2018 (152)
45 ClinVar RCV000656380.1 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
ss491939749 NC_000009.10:100634049:G= NC_000009.12:98831946:G= (self)
47045375, 26132426, 18577599, 9706841, 221855005, 5494603, 905541, 26132426, ss335691697, ss342278397, ss490981426, ss491425306, ss780878739, ss783564313, ss986791826, ss1334752829, ss1623183991, ss1666178024, ss1689576516, ss1711231233, ss1752749356, ss1917838468, ss1946263713, ss1959200217, ss2483447327, ss2737747992, ss2748230602, ss2881227250, ss2985467837, ss3005305323, ss3022947471, ss3625987685, ss3630313875, ss3635223577, ss3640930868, ss3644997041, ss3653500964, ss3654232652 NC_000009.11:101594228:G= NC_000009.12:98831946:G= (self)
416367563, ss2312970171, ss3596040101 NC_000009.12:98831946:G= NC_000009.12:98831946:G= (self)
ss491939749 NC_000009.10:100634049:G>A NC_000009.12:98831946:G>A (self)
47045375, 26132426, 18577599, 9706841, 221855005, 5494603, 905541, 26132426, ss335691697, ss342278397, ss490981426, ss491425306, ss780878739, ss783564313, ss986791826, ss1334752829, ss1623183991, ss1666178024, ss1689576516, ss1711231233, ss1752749356, ss1917838468, ss1946263713, ss1959200217, ss2483447327, ss2737747992, ss2748230602, ss2881227250, ss2985467837, ss3005305323, ss3022947471, ss3625987685, ss3630313875, ss3635223577, ss3640930868, ss3644997041, ss3653500964, ss3654232652 NC_000009.11:101594228:G>A NC_000009.12:98831946:G>A (self)
RCV000210098.1, RCV000229689.2, RCV000656380.1, 416367563, ss2312970171, ss3596040101 NC_000009.12:98831946:G>A NC_000009.12:98831946: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.

1 citation for rs145236923
PMID Title Author Year Journal
26845104 Improving performance of multigene panels for genomic analysis of cancer predisposition. Shirts BH et al. 2016 Genetics in medicine

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.post58+e54ea20