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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.

rs767418527

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr9:35092532 (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
G>A / G>C
Variation Type
SNV Single Nucleotide Variation
Frequency
A=0.000019 (5/264690, TOPMED)
A=0.000014 (2/140300, GnomAD)
A=0.00001 (1/78696, PAGE_STUDY) (+ 2 more)
A=0.00005 (1/19180, ALFA)
A=0.0002 (1/4480, Estonian)
Clinical Significance
Reported in ClinVar
Gene : Consequence
PIGO : 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 19180 G=0.99995 A=0.00005
European Sub 14230 G=0.99993 A=0.00007
African Sub 3332 G=1.0000 A=0.0000
African Others Sub 114 G=1.000 A=0.000
African American Sub 3218 G=1.0000 A=0.0000
Asian Sub 146 G=1.000 A=0.000
East Asian Sub 120 G=1.000 A=0.000
Other Asian Sub 26 G=1.00 A=0.00
Latin American 1 Sub 146 G=1.000 A=0.000
Latin American 2 Sub 610 G=1.000 A=0.000
South Asian Sub 104 G=1.000 A=0.000
Other Sub 612 G=1.000 A=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 G=0.999981 A=0.000019
gnomAD - Genomes Global Study-wide 140300 G=0.999986 A=0.000014
gnomAD - Genomes European Sub 75966 G=0.99999 A=0.00001
gnomAD - Genomes African Sub 42054 G=0.99998 A=0.00002
gnomAD - Genomes American Sub 13668 G=1.00000 A=0.00000
gnomAD - Genomes Ashkenazi Jewish Sub 3324 G=1.0000 A=0.0000
gnomAD - Genomes East Asian Sub 3134 G=1.0000 A=0.0000
gnomAD - Genomes Other Sub 2154 G=1.0000 A=0.0000
The PAGE Study Global Study-wide 78696 G=0.99999 A=0.00001
The PAGE Study AfricanAmerican Sub 32516 G=0.99997 A=0.00003
The PAGE Study Mexican Sub 10810 G=1.00000 A=0.00000
The PAGE Study Asian Sub 8316 G=1.0000 A=0.0000
The PAGE Study PuertoRican Sub 7916 G=1.0000 A=0.0000
The PAGE Study NativeHawaiian Sub 4534 G=1.0000 A=0.0000
The PAGE Study Cuban Sub 4230 G=1.0000 A=0.0000
The PAGE Study Dominican Sub 3826 G=1.0000 A=0.0000
The PAGE Study CentralAmerican Sub 2450 G=1.0000 A=0.0000
The PAGE Study SouthAmerican Sub 1982 G=1.0000 A=0.0000
The PAGE Study NativeAmerican Sub 1260 G=1.0000 A=0.0000
The PAGE Study SouthAsian Sub 856 G=1.000 A=0.000
Allele Frequency Aggregator Total Global 19180 G=0.99995 A=0.00005
Allele Frequency Aggregator European Sub 14230 G=0.99993 A=0.00007
Allele Frequency Aggregator African Sub 3332 G=1.0000 A=0.0000
Allele Frequency Aggregator Other Sub 612 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 2 Sub 610 G=1.000 A=0.000
Allele Frequency Aggregator Latin American 1 Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator Asian Sub 146 G=1.000 A=0.000
Allele Frequency Aggregator South Asian Sub 104 G=1.000 A=0.000
Genetic variation in the Estonian population Estonian Study-wide 4480 G=0.9998 A=0.0002
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 9 NC_000009.12:g.35092532G>A
GRCh38.p14 chr 9 NC_000009.12:g.35092532G>C
GRCh37.p13 chr 9 NC_000009.11:g.35092529G>A
GRCh37.p13 chr 9 NC_000009.11:g.35092529G>C
PIGO RefSeqGene NG_031990.1:g.9070C>T
PIGO RefSeqGene NG_031990.1:g.9070C>G
Gene: PIGO, phosphatidylinositol glycan anchor biosynthesis class O (minus strand)
Molecule type Change Amino acid[Codon] SO Term
PIGO transcript variant 3 NM_001201484.2:c.1344+11C…

NM_001201484.2:c.1344+11C>T

N/A Intron Variant
PIGO transcript variant 2 NM_152850.4:c.1344+11C>T N/A Intron Variant
PIGO transcript variant 1 NM_032634.4:c.1355C>T A [GCG] > V [GTG] Coding Sequence Variant
GPI ethanolamine phosphate transferase 3 isoform 1 NP_116023.2:p.Ala452Val A (Ala) > V (Val) Missense Variant
PIGO transcript variant 1 NM_032634.4:c.1355C>G A [GCG] > G [GGG] Coding Sequence Variant
GPI ethanolamine phosphate transferase 3 isoform 1 NP_116023.2:p.Ala452Gly A (Ala) > G (Gly) Missense Variant
PIGO transcript variant X1 XM_005251619.4:c.1355C>T A [GCG] > V [GTG] Coding Sequence Variant
GPI ethanolamine phosphate transferase 3 isoform X1 XP_005251676.1:p.Ala452Val A (Ala) > V (Val) Missense Variant
PIGO transcript variant X1 XM_005251619.4:c.1355C>G A [GCG] > G [GGG] Coding Sequence Variant
GPI ethanolamine phosphate transferase 3 isoform X1 XP_005251676.1:p.Ala452Gly A (Ala) > G (Gly) Missense Variant
PIGO transcript variant X2 XM_047423974.1:c.1355C>T A [GCG] > V [GTG] Coding Sequence Variant
GPI ethanolamine phosphate transferase 3 isoform X2 XP_047279930.1:p.Ala452Val A (Ala) > V (Val) Missense Variant
PIGO transcript variant X2 XM_047423974.1:c.1355C>G A [GCG] > G [GGG] Coding Sequence Variant
GPI ethanolamine phosphate transferase 3 isoform X2 XP_047279930.1:p.Ala452Gly A (Ala) > G (Gly) 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: 993458 )
ClinVar Accession Disease Names Clinical Significance
RCV001298756.4 Hyperphosphatasia with intellectual disability syndrome 2 Uncertain-Significance
Allele: C (allele ID: 1475739 )
ClinVar Accession Disease Names Clinical Significance
RCV002019352.1 Hyperphosphatasia with intellectual disability syndrome 2 Uncertain-Significance
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 C
GRCh38.p14 chr 9 NC_000009.12:g.35092532= NC_000009.12:g.35092532G>A NC_000009.12:g.35092532G>C
GRCh37.p13 chr 9 NC_000009.11:g.35092529= NC_000009.11:g.35092529G>A NC_000009.11:g.35092529G>C
PIGO RefSeqGene NG_031990.1:g.9070= NG_031990.1:g.9070C>T NG_031990.1:g.9070C>G
PIGO transcript variant 1 NM_032634.4:c.1355= NM_032634.4:c.1355C>T NM_032634.4:c.1355C>G
PIGO transcript variant 1 NM_032634.3:c.1355= NM_032634.3:c.1355C>T NM_032634.3:c.1355C>G
PIGO transcript variant X1 XM_005251619.4:c.1355= XM_005251619.4:c.1355C>T XM_005251619.4:c.1355C>G
PIGO transcript variant X1 XM_005251619.3:c.1355= XM_005251619.3:c.1355C>T XM_005251619.3:c.1355C>G
PIGO transcript variant X1 XM_005251619.2:c.1355= XM_005251619.2:c.1355C>T XM_005251619.2:c.1355C>G
PIGO transcript variant X1 XM_005251619.1:c.1355= XM_005251619.1:c.1355C>T XM_005251619.1:c.1355C>G
PIGO transcript variant X2 XM_047423974.1:c.1355= XM_047423974.1:c.1355C>T XM_047423974.1:c.1355C>G
GPI ethanolamine phosphate transferase 3 isoform 1 NP_116023.2:p.Ala452= NP_116023.2:p.Ala452Val NP_116023.2:p.Ala452Gly
GPI ethanolamine phosphate transferase 3 isoform X1 XP_005251676.1:p.Ala452= XP_005251676.1:p.Ala452Val XP_005251676.1:p.Ala452Gly
GPI ethanolamine phosphate transferase 3 isoform X2 XP_047279930.1:p.Ala452= XP_047279930.1:p.Ala452Val XP_047279930.1:p.Ala452Gly
PIGO transcript variant 3 NM_001201484.1:c.1344+11= NM_001201484.1:c.1344+11C>T NM_001201484.1:c.1344+11C>G
PIGO transcript variant 3 NM_001201484.2:c.1344+11= NM_001201484.2:c.1344+11C>T NM_001201484.2:c.1344+11C>G
PIGO transcript variant 2 NM_152850.3:c.1344+11= NM_152850.3:c.1344+11C>T NM_152850.3:c.1344+11C>G
PIGO transcript variant 2 NM_152850.4:c.1344+11= NM_152850.4:c.1344+11C>T NM_152850.4:c.1344+11C>G
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#.

12 SubSNP, 9 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1689471101 Apr 01, 2015 (144)
2 EVA_EXAC ss1689471102 Apr 01, 2015 (144)
3 ILLUMINA ss1959180413 Feb 12, 2016 (147)
4 GNOMAD ss2737582639 Nov 08, 2017 (151)
5 GNOMAD ss2748178052 Nov 08, 2017 (151)
6 GNOMAD ss2877691732 Nov 08, 2017 (151)
7 ILLUMINA ss3022925342 Nov 08, 2017 (151)
8 ILLUMINA ss3653477532 Oct 12, 2018 (152)
9 EGCUT_WGS ss3672453620 Jul 13, 2019 (153)
10 ILLUMINA ss3726608950 Jul 13, 2019 (153)
11 PAGE_CC ss3771498128 Jul 13, 2019 (153)
12 TOPMED ss4819729046 Apr 26, 2021 (155)
13 Genetic variation in the Estonian population NC_000009.11 - 35092529 Oct 12, 2018 (152)
14 ExAC

Submission ignored due to conflicting rows:
Row 9592442 (NC_000009.11:35092528:G:G 121009/121012, NC_000009.11:35092528:G:A 3/121012)
Row 9592443 (NC_000009.11:35092528:G:G 121011/121012, NC_000009.11:35092528:G:C 1/121012)

- Oct 12, 2018 (152)
15 ExAC

Submission ignored due to conflicting rows:
Row 9592442 (NC_000009.11:35092528:G:G 121009/121012, NC_000009.11:35092528:G:A 3/121012)
Row 9592443 (NC_000009.11:35092528:G:G 121011/121012, NC_000009.11:35092528:G:C 1/121012)

- Oct 12, 2018 (152)
16 gnomAD - Genomes NC_000009.12 - 35092532 Apr 26, 2021 (155)
17 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 6765368 (NC_000009.11:35092528:G:G 250893/250896, NC_000009.11:35092528:G:A 3/250896)
Row 6765369 (NC_000009.11:35092528:G:G 250895/250896, NC_000009.11:35092528:G:C 1/250896)

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

Submission ignored due to conflicting rows:
Row 6765368 (NC_000009.11:35092528:G:G 250893/250896, NC_000009.11:35092528:G:A 3/250896)
Row 6765369 (NC_000009.11:35092528:G:G 250895/250896, NC_000009.11:35092528:G:C 1/250896)

- Jul 13, 2019 (153)
19 The PAGE Study NC_000009.12 - 35092532 Jul 13, 2019 (153)
20 TopMed NC_000009.12 - 35092532 Apr 26, 2021 (155)
21 ALFA NC_000009.12 - 35092532 Apr 26, 2021 (155)
22 ClinVar RCV001298756.4 Oct 16, 2022 (156)
23 ClinVar RCV002019352.1 Oct 16, 2022 (156)
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
18191868, ss1689471101, ss1959180413, ss2737582639, ss2748178052, ss2877691732, ss3022925342, ss3653477532, ss3672453620 NC_000009.11:35092528:G:A NC_000009.12:35092531:G:A (self)
RCV001298756.4, 323918610, 719597, 657106607, 9889020962, ss3726608950, ss3771498128, ss4819729046 NC_000009.12:35092531:G:A NC_000009.12:35092531:G:A (self)
ss1689471102, ss2737582639 NC_000009.11:35092528:G:C NC_000009.12:35092531:G:C (self)
RCV002019352.1 NC_000009.12:35092531:G:C NC_000009.12:35092531:G:C
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 rs767418527

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