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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.

rs119103238

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:184245333 (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
A>G / A>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.000011 (3/264690, TOPMED)
G=0.000008 (2/245852, GnomAD_exome)
G=0.000018 (2/113070, ExAC) (+ 3 more)
T=0.00000 (0/78696, PAGE_STUDY)
T=0.00000 (0/10680, ALFA)
G=0.0003 (1/2922, KOREAN)
Clinical Significance
Reported in ClinVar
Gene : Consequence
ALG3 : Missense Variant
Publications
1 citation
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 10680 A=1.00000 T=0.00000
European Sub 6962 A=1.0000 T=0.0000
African Sub 2294 A=1.0000 T=0.0000
African Others Sub 84 A=1.00 T=0.00
African American Sub 2210 A=1.0000 T=0.0000
Asian Sub 108 A=1.000 T=0.000
East Asian Sub 84 A=1.00 T=0.00
Other Asian Sub 24 A=1.00 T=0.00
Latin American 1 Sub 146 A=1.000 T=0.000
Latin American 2 Sub 610 A=1.000 T=0.000
South Asian Sub 94 A=1.00 T=0.00
Other Sub 466 A=1.000 T=0.000


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 A=0.999989 T=0.000011
gnomAD - Exomes Global Study-wide 245852 A=0.999992 G=0.000008
gnomAD - Exomes European Sub 132476 A=1.000000 G=0.000000
gnomAD - Exomes Asian Sub 48128 A=0.99996 G=0.00004
gnomAD - Exomes American Sub 34098 A=1.00000 G=0.00000
gnomAD - Exomes African Sub 15158 A=1.00000 G=0.00000
gnomAD - Exomes Ashkenazi Jewish Sub 9994 A=1.0000 G=0.0000
gnomAD - Exomes Other Sub 5998 A=1.0000 G=0.0000
ExAC Global Study-wide 113070 A=0.999982 G=0.000018
ExAC Europe Sub 68966 A=1.00000 G=0.00000
ExAC Asian Sub 23756 A=0.99992 G=0.00008
ExAC American Sub 10530 A=1.00000 G=0.00000
ExAC African Sub 8982 A=1.0000 G=0.0000
ExAC Other Sub 836 A=1.000 G=0.000
The PAGE Study Global Study-wide 78696 A=1.00000 T=0.00000
The PAGE Study AfricanAmerican Sub 32516 A=1.00000 T=0.00000
The PAGE Study Mexican Sub 10810 A=1.00000 T=0.00000
The PAGE Study Asian Sub 8314 A=1.0000 T=0.0000
The PAGE Study PuertoRican Sub 7918 A=1.0000 T=0.0000
The PAGE Study NativeHawaiian Sub 4532 A=1.0000 T=0.0000
The PAGE Study Cuban Sub 4230 A=1.0000 T=0.0000
The PAGE Study Dominican Sub 3828 A=1.0000 T=0.0000
The PAGE Study CentralAmerican Sub 2450 A=1.0000 T=0.0000
The PAGE Study SouthAmerican Sub 1982 A=1.0000 T=0.0000
The PAGE Study NativeAmerican Sub 1260 A=1.0000 T=0.0000
The PAGE Study SouthAsian Sub 856 A=1.000 T=0.000
Allele Frequency Aggregator Total Global 10680 A=1.00000 T=0.00000
Allele Frequency Aggregator European Sub 6962 A=1.0000 T=0.0000
Allele Frequency Aggregator African Sub 2294 A=1.0000 T=0.0000
Allele Frequency Aggregator Latin American 2 Sub 610 A=1.000 T=0.000
Allele Frequency Aggregator Other Sub 466 A=1.000 T=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 A=1.000 T=0.000
Allele Frequency Aggregator Asian Sub 108 A=1.000 T=0.000
Allele Frequency Aggregator South Asian Sub 94 A=1.00 T=0.00
KOREAN population from KRGDB KOREAN Study-wide 2922 A=0.9997 G=0.0003
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.184245333A>G
GRCh38.p14 chr 3 NC_000003.12:g.184245333A>T
GRCh37.p13 chr 3 NC_000003.11:g.183963121A>G
GRCh37.p13 chr 3 NC_000003.11:g.183963121A>T
ALG3 RefSeqGene NG_008924.2:g.9180T>C
ALG3 RefSeqGene NG_008924.2:g.9180T>A
Gene: ALG3, ALG3 alpha-1,3- mannosyltransferase (minus strand)
Molecule type Change Amino acid[Codon] SO Term
ALG3 transcript variant 4 NM_001006941.2:c.326T>C M [ATG] > T [ACG] Coding Sequence Variant
dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase isoform d NP_001006942.1:p.Met109Thr M (Met) > T (Thr) Missense Variant
ALG3 transcript variant 4 NM_001006941.2:c.326T>A M [ATG] > K [AAG] Coding Sequence Variant
dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase isoform d NP_001006942.1:p.Met109Lys M (Met) > K (Lys) Missense Variant
ALG3 transcript variant 1 NM_005787.6:c.470T>C M [ATG] > T [ACG] Coding Sequence Variant
dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase isoform a NP_005778.1:p.Met157Thr M (Met) > T (Thr) Missense Variant
ALG3 transcript variant 1 NM_005787.6:c.470T>A M [ATG] > K [AAG] Coding Sequence Variant
dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase isoform a NP_005778.1:p.Met157Lys M (Met) > K (Lys) Missense Variant
ALG3 transcript variant 5 NR_024533.1:n.401T>C N/A Non Coding Transcript Variant
ALG3 transcript variant 5 NR_024533.1:n.401T>A N/A Non Coding Transcript Variant
ALG3 transcript variant 2 NR_024534.1:n.464T>C N/A Non Coding Transcript Variant
ALG3 transcript variant 2 NR_024534.1:n.464T>A N/A Non Coding 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: 17170 )
ClinVar Accession Disease Names Clinical Significance
RCV000002213.4 ALG3-CDG Pathogenic
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 A= G T
GRCh38.p14 chr 3 NC_000003.12:g.184245333= NC_000003.12:g.184245333A>G NC_000003.12:g.184245333A>T
GRCh37.p13 chr 3 NC_000003.11:g.183963121= NC_000003.11:g.183963121A>G NC_000003.11:g.183963121A>T
ALG3 RefSeqGene NG_008924.2:g.9180= NG_008924.2:g.9180T>C NG_008924.2:g.9180T>A
ALG3 transcript variant 1 NM_005787.6:c.470= NM_005787.6:c.470T>C NM_005787.6:c.470T>A
ALG3 transcript variant 1 NM_005787.5:c.470= NM_005787.5:c.470T>C NM_005787.5:c.470T>A
ALG3 transcript variant 4 NM_001006941.2:c.326= NM_001006941.2:c.326T>C NM_001006941.2:c.326T>A
ALG3 transcript variant 2 NR_024534.1:n.464= NR_024534.1:n.464T>C NR_024534.1:n.464T>A
ALG3 transcript variant 5 NR_024533.1:n.401= NR_024533.1:n.401T>C NR_024533.1:n.401T>A
ALG3 transcript variant 3 NM_001006940.1:c.350= NM_001006940.1:c.350T>C NM_001006940.1:c.350T>A
ALG3 transcript variant 2 NM_001006942.1:c.365= NM_001006942.1:c.365T>C NM_001006942.1:c.365T>A
dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase isoform a NP_005778.1:p.Met157= NP_005778.1:p.Met157Thr NP_005778.1:p.Met157Lys
dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase isoform d NP_001006942.1:p.Met109= NP_001006942.1:p.Met109Thr NP_001006942.1:p.Met109Lys
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#.

11 SubSNP, 6 Frequency, 1 ClinVar submissions
No Submitter Submission ID Date (Build)
1 OMIM-CURATED-RECORDS ss253283153 Aug 18, 2010 (132)
2 EVA_EXAC ss1687316942 Apr 01, 2015 (144)
3 ILLUMINA ss1958636342 Feb 12, 2016 (147)
4 HUMAN_LONGEVITY ss2258891949 Dec 20, 2016 (150)
5 GNOMAD ss2734237821 Nov 08, 2017 (151)
6 ILLUMINA ss3022321812 Nov 08, 2017 (151)
7 ILLUMINA ss3652803166 Oct 12, 2018 (152)
8 ILLUMINA ss3726089095 Jul 13, 2019 (153)
9 PAGE_CC ss3771089087 Jul 13, 2019 (153)
10 KRGDB ss3903829250 Apr 25, 2020 (154)
11 TOPMED ss4596405469 Apr 26, 2021 (155)
12 ExAC NC_000003.11 - 183963121 Oct 12, 2018 (152)
13 gnomAD - Exomes NC_000003.11 - 183963121 Jul 13, 2019 (153)
14 KOREAN population from KRGDB NC_000003.11 - 183963121 Apr 25, 2020 (154)
15 The PAGE Study NC_000003.12 - 184245333 Jul 13, 2019 (153)
16 TopMed NC_000003.12 - 184245333 Apr 26, 2021 (155)
17 ALFA NC_000003.12 - 184245333 Apr 26, 2021 (155)
18 ClinVar RCV000002213.4 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
7265804, 3331093, 11006644, ss1687316942, ss2734237821, ss3903829250 NC_000003.11:183963120:A:G NC_000003.12:184245332:A:G (self)
ss1958636342, ss3022321812, ss3652803166 NC_000003.11:183963120:A:T NC_000003.12:184245332:A:T (self)
RCV000002213.4, 310556, 433783024, 12309402250, ss253283153, ss2258891949, ss3726089095, ss3771089087, ss4596405469 NC_000003.12:184245332:A:T NC_000003.12:184245332:A: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 rs119103238
PMID Title Author Year Journal
17551933 CDG-Id in two siblings with partially different phenotypes. Kranz C et al. 2007 American journal of medical genetics. Part A
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