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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.

rs143214380

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr3:37323890 (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
Variation Type
SNV Single Nucleotide Variation
Frequency
G=0.000015 (4/264690, TOPMED)
G=0.000008 (2/249130, GnomAD_exome)
G=0.000007 (1/140278, GnomAD) (+ 2 more)
G=0.00003 (1/35432, ALFA)
G=0.00008 (1/12996, GO-ESP)
Clinical Significance
Not Reported in ClinVar
Gene : Consequence
GOLGA4 : Missense Variant
Publications
0 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 35432 A=0.99997 G=0.00003
European Sub 26588 A=0.99996 G=0.00004
African Sub 2918 A=1.0000 G=0.0000
African Others Sub 114 A=1.000 G=0.000
African American Sub 2804 A=1.0000 G=0.0000
Asian Sub 112 A=1.000 G=0.000
East Asian Sub 86 A=1.00 G=0.00
Other Asian Sub 26 A=1.00 G=0.00
Latin American 1 Sub 500 A=1.000 G=0.000
Latin American 2 Sub 628 A=1.000 G=0.000
South Asian Sub 98 A=1.00 G=0.00
Other Sub 4588 A=1.0000 G=0.0000


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=0.999985 G=0.000015
gnomAD - Exomes Global Study-wide 249130 A=0.999992 G=0.000008
gnomAD - Exomes European Sub 134294 A=0.999993 G=0.000007
gnomAD - Exomes Asian Sub 48792 A=1.00000 G=0.00000
gnomAD - Exomes American Sub 34438 A=1.00000 G=0.00000
gnomAD - Exomes African Sub 15524 A=0.99994 G=0.00006
gnomAD - Exomes Ashkenazi Jewish Sub 10036 A=1.00000 G=0.00000
gnomAD - Exomes Other Sub 6046 A=1.0000 G=0.0000
gnomAD - Genomes Global Study-wide 140278 A=0.999993 G=0.000007
gnomAD - Genomes European Sub 75952 A=1.00000 G=0.00000
gnomAD - Genomes African Sub 42062 A=0.99998 G=0.00002
gnomAD - Genomes American Sub 13656 A=1.00000 G=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3322 A=1.0000 G=0.0000
gnomAD - Genomes East Asian Sub 3132 A=1.0000 G=0.0000
gnomAD - Genomes Other Sub 2154 A=1.0000 G=0.0000
Allele Frequency Aggregator Total Global 35432 A=0.99997 G=0.00003
Allele Frequency Aggregator European Sub 26588 A=0.99996 G=0.00004
Allele Frequency Aggregator Other Sub 4588 A=1.0000 G=0.0000
Allele Frequency Aggregator African Sub 2918 A=1.0000 G=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 A=1.000 G=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 A=1.000 G=0.000
Allele Frequency Aggregator Asian Sub 112 A=1.000 G=0.000
Allele Frequency Aggregator South Asian Sub 98 A=1.00 G=0.00
GO Exome Sequencing Project Global Study-wide 12996 A=0.99992 G=0.00008
GO Exome Sequencing Project European American Sub 8598 A=0.9999 G=0.0001
GO Exome Sequencing Project African American Sub 4398 A=1.0000 G=0.0000
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.37323890A>G
GRCh37.p13 chr 3 NC_000003.11:g.37365381A>G
GOLGA4 RefSeqGene NG_047053.1:g.85700A>G
Gene: GOLGA4, golgin A4 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GOLGA4 transcript variant 2 NM_002078.5:c.2004A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform 2 NP_002069.2:p.Ile668Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant 1 NM_001172713.2:c.2070A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform 1 NP_001166184.1:p.Ile690Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X1 XM_005265069.4:c.2169A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X1 XP_005265126.1:p.Ile723Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X2 XM_005265070.4:c.2169A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X2 XP_005265127.1:p.Ile723Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X3 XM_005265071.4:c.2169A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X3 XP_005265128.1:p.Ile723Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X4 XM_017006184.2:c.2169A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X4 XP_016861673.1:p.Ile723Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X5 XM_005265072.4:c.2121A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X5 XP_005265129.1:p.Ile707Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X6 XM_005265073.2:c.2070A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X6 XP_005265130.1:p.Ile690Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X7 XM_047447980.1:c.2067A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X7 XP_047303936.1:p.Ile689Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X8 XM_047447981.1:c.2067A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X7 XP_047303937.1:p.Ile689Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X9 XM_047447982.1:c.2070A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X8 XP_047303938.1:p.Ile690Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X9 XM_006713110.3:c.2064A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X8 XP_006713173.1:p.Ile688Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X10 XM_005265074.2:c.2070A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X9 XP_005265131.1:p.Ile690Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X11 XM_017006187.2:c.2022A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X10 XP_016861676.1:p.Ile674Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X12 XM_047447983.1:c.2022A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X11 XP_047303939.1:p.Ile674Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X13 XM_047447984.1:c.2004A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X12 XP_047303940.1:p.Ile668Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X14 XM_047447985.1:c.1965A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X13 XP_047303941.1:p.Ile655Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X15 XM_047447986.1:c.1965A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X14 XP_047303942.1:p.Ile655Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X16 XM_005265075.2:c.1956A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X15 XP_005265132.1:p.Ile652Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X17 XM_017006188.2:c.1899A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X16 XP_016861677.1:p.Ile633Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X18 XM_024453457.2:c.1647A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X17 XP_024309225.1:p.Ile549Met I (Ile) > M (Met) Missense Variant
GOLGA4 transcript variant X19 XM_011533598.4:c.693A>G I [ATA] > M [ATG] Coding Sequence Variant
golgin subfamily A member 4 isoform X18 XP_011531900.1:p.Ile231Met I (Ile) > M (Met) 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.

Not Reported in ClinVar
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
GRCh38.p14 chr 3 NC_000003.12:g.37323890= NC_000003.12:g.37323890A>G
GRCh37.p13 chr 3 NC_000003.11:g.37365381= NC_000003.11:g.37365381A>G
GOLGA4 RefSeqGene NG_047053.1:g.85700= NG_047053.1:g.85700A>G
GOLGA4 transcript variant 2 NM_002078.5:c.2004= NM_002078.5:c.2004A>G
GOLGA4 transcript variant 2 NM_002078.4:c.2004= NM_002078.4:c.2004A>G
GOLGA4 transcript variant 1 NM_001172713.2:c.2070= NM_001172713.2:c.2070A>G
GOLGA4 transcript variant 1 NM_001172713.1:c.2070= NM_001172713.1:c.2070A>G
GOLGA4 transcript variant 3 NM_001410721.1:c.2070= NM_001410721.1:c.2070A>G
GOLGA4 transcript variant X1 XM_005265069.4:c.2169= XM_005265069.4:c.2169A>G
GOLGA4 transcript variant X1 XM_005265069.3:c.2169= XM_005265069.3:c.2169A>G
GOLGA4 transcript variant X1 XM_005265069.2:c.2169= XM_005265069.2:c.2169A>G
GOLGA4 transcript variant X1 XM_005265069.1:c.2169= XM_005265069.1:c.2169A>G
GOLGA4 transcript variant X3 XM_005265071.4:c.2169= XM_005265071.4:c.2169A>G
GOLGA4 transcript variant X3 XM_005265071.3:c.2169= XM_005265071.3:c.2169A>G
GOLGA4 transcript variant X3 XM_005265071.2:c.2169= XM_005265071.2:c.2169A>G
GOLGA4 transcript variant X3 XM_005265071.1:c.2169= XM_005265071.1:c.2169A>G
GOLGA4 transcript variant X5 XM_005265072.4:c.2121= XM_005265072.4:c.2121A>G
GOLGA4 transcript variant X5 XM_005265072.3:c.2121= XM_005265072.3:c.2121A>G
GOLGA4 transcript variant X4 XM_005265072.2:c.2121= XM_005265072.2:c.2121A>G
GOLGA4 transcript variant X4 XM_005265072.1:c.2121= XM_005265072.1:c.2121A>G
GOLGA4 transcript variant X2 XM_005265070.4:c.2169= XM_005265070.4:c.2169A>G
GOLGA4 transcript variant X2 XM_005265070.3:c.2169= XM_005265070.3:c.2169A>G
GOLGA4 transcript variant X2 XM_005265070.2:c.2169= XM_005265070.2:c.2169A>G
GOLGA4 transcript variant X2 XM_005265070.1:c.2169= XM_005265070.1:c.2169A>G
GOLGA4 transcript variant X19 XM_011533598.4:c.693= XM_011533598.4:c.693A>G
GOLGA4 transcript variant X17 XM_011533598.3:c.693= XM_011533598.3:c.693A>G
GOLGA4 transcript variant X14 XM_011533598.2:c.693= XM_011533598.2:c.693A>G
GOLGA4 transcript variant X10 XM_011533598.1:c.693= XM_011533598.1:c.693A>G
GOLGA4 transcript variant X9 XM_006713110.3:c.2064= XM_006713110.3:c.2064A>G
GOLGA4 transcript variant X9 XM_006713110.2:c.2064= XM_006713110.2:c.2064A>G
GOLGA4 transcript variant X8 XM_006713110.1:c.2064= XM_006713110.1:c.2064A>G
GOLGA4 transcript variant X18 XM_024453457.2:c.1647= XM_024453457.2:c.1647A>G
GOLGA4 transcript variant X15 XM_024453457.1:c.1647= XM_024453457.1:c.1647A>G
GOLGA4 transcript variant X4 XM_017006184.2:c.2169= XM_017006184.2:c.2169A>G
GOLGA4 transcript variant X4 XM_017006184.1:c.2169= XM_017006184.1:c.2169A>G
GOLGA4 transcript variant X6 XM_005265073.2:c.2070= XM_005265073.2:c.2070A>G
GOLGA4 transcript variant X6 XM_005265073.1:c.2070= XM_005265073.1:c.2070A>G
GOLGA4 transcript variant X10 XM_005265074.2:c.2070= XM_005265074.2:c.2070A>G
GOLGA4 transcript variant X10 XM_005265074.1:c.2070= XM_005265074.1:c.2070A>G
GOLGA4 transcript variant X11 XM_017006187.2:c.2022= XM_017006187.2:c.2022A>G
GOLGA4 transcript variant X11 XM_017006187.1:c.2022= XM_017006187.1:c.2022A>G
GOLGA4 transcript variant X16 XM_005265075.2:c.1956= XM_005265075.2:c.1956A>G
GOLGA4 transcript variant X12 XM_005265075.1:c.1956= XM_005265075.1:c.1956A>G
GOLGA4 transcript variant X17 XM_017006188.2:c.1899= XM_017006188.2:c.1899A>G
GOLGA4 transcript variant X13 XM_017006188.1:c.1899= XM_017006188.1:c.1899A>G
GOLGA4 transcript variant X8 XM_047447981.1:c.2067= XM_047447981.1:c.2067A>G
GOLGA4 transcript variant X7 XM_047447980.1:c.2067= XM_047447980.1:c.2067A>G
GOLGA4 transcript variant X9 XM_047447982.1:c.2070= XM_047447982.1:c.2070A>G
GOLGA4 transcript variant X14 XM_047447985.1:c.1965= XM_047447985.1:c.1965A>G
GOLGA4 transcript variant X12 XM_047447983.1:c.2022= XM_047447983.1:c.2022A>G
GOLGA4 transcript variant X13 XM_047447984.1:c.2004= XM_047447984.1:c.2004A>G
GOLGA4 transcript variant X15 XM_047447986.1:c.1965= XM_047447986.1:c.1965A>G
golgin subfamily A member 4 isoform 2 NP_002069.2:p.Ile668= NP_002069.2:p.Ile668Met
golgin subfamily A member 4 isoform 1 NP_001166184.1:p.Ile690= NP_001166184.1:p.Ile690Met
golgin subfamily A member 4 isoform X1 XP_005265126.1:p.Ile723= XP_005265126.1:p.Ile723Met
golgin subfamily A member 4 isoform X3 XP_005265128.1:p.Ile723= XP_005265128.1:p.Ile723Met
golgin subfamily A member 4 isoform X5 XP_005265129.1:p.Ile707= XP_005265129.1:p.Ile707Met
golgin subfamily A member 4 isoform X2 XP_005265127.1:p.Ile723= XP_005265127.1:p.Ile723Met
golgin subfamily A member 4 isoform X18 XP_011531900.1:p.Ile231= XP_011531900.1:p.Ile231Met
golgin subfamily A member 4 isoform X8 XP_006713173.1:p.Ile688= XP_006713173.1:p.Ile688Met
golgin subfamily A member 4 isoform X17 XP_024309225.1:p.Ile549= XP_024309225.1:p.Ile549Met
golgin subfamily A member 4 isoform X4 XP_016861673.1:p.Ile723= XP_016861673.1:p.Ile723Met
golgin subfamily A member 4 isoform X6 XP_005265130.1:p.Ile690= XP_005265130.1:p.Ile690Met
golgin subfamily A member 4 isoform X9 XP_005265131.1:p.Ile690= XP_005265131.1:p.Ile690Met
golgin subfamily A member 4 isoform X10 XP_016861676.1:p.Ile674= XP_016861676.1:p.Ile674Met
golgin subfamily A member 4 isoform X15 XP_005265132.1:p.Ile652= XP_005265132.1:p.Ile652Met
golgin subfamily A member 4 isoform X16 XP_016861677.1:p.Ile633= XP_016861677.1:p.Ile633Met
golgin subfamily A member 4 isoform X7 XP_047303937.1:p.Ile689= XP_047303937.1:p.Ile689Met
golgin subfamily A member 4 isoform X7 XP_047303936.1:p.Ile689= XP_047303936.1:p.Ile689Met
golgin subfamily A member 4 isoform X8 XP_047303938.1:p.Ile690= XP_047303938.1:p.Ile690Met
golgin subfamily A member 4 isoform X13 XP_047303941.1:p.Ile655= XP_047303941.1:p.Ile655Met
golgin subfamily A member 4 isoform X11 XP_047303939.1:p.Ile674= XP_047303939.1:p.Ile674Met
golgin subfamily A member 4 isoform X12 XP_047303940.1:p.Ile668= XP_047303940.1:p.Ile668Met
golgin subfamily A member 4 isoform X14 XP_047303942.1:p.Ile655= XP_047303942.1:p.Ile655Met
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#.

5 SubSNP, 5 Frequency submissions
No Submitter Submission ID Date (Build)
1 NHLBI-ESP ss342119193 May 09, 2011 (134)
2 GNOMAD ss2733624313 Nov 08, 2017 (151)
3 EVA ss3823895323 Apr 25, 2020 (154)
4 GNOMAD ss4069170381 Apr 27, 2021 (155)
5 TOPMED ss4560895128 Apr 27, 2021 (155)
6 gnomAD - Genomes NC_000003.12 - 37323890 Apr 27, 2021 (155)
7 gnomAD - Exomes NC_000003.11 - 37365381 Jul 13, 2019 (153)
8 GO Exome Sequencing Project NC_000003.11 - 37365381 Oct 12, 2018 (152)
9 TopMed NC_000003.12 - 37323890 Apr 27, 2021 (155)
10 ALFA NC_000003.12 - 37323890 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
2698344, 353684, ss342119193, ss2733624313, ss3823895323 NC_000003.11:37365380:A:G NC_000003.12:37323889:A:G (self)
104622439, 398272683, 4908763263, ss4069170381, ss4560895128 NC_000003.12:37323889:A:G NC_000003.12:37323889:A:G (self)
Help

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

No publications for rs143214380

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