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dbSNP Short Genetic Variations

Examples: rs268, BRCA1 and more Advanced search

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.

rs775157869

Current Build 156

Released September 21, 2022

Organism
Homo sapiens
Position
chr5:161897258 (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=0.000011 (3/264690, TOPMED)
A=0.00005 (2/44420, ALFA)
Clinical Significance
Reported in ClinVar
Gene : Consequence
GABRA1 : 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 60780 G=0.99995 A=0.00005, C=0.00000
European Sub 42740 G=0.99993 A=0.00007, C=0.00000
African Sub 8348 G=1.0000 A=0.0000, C=0.0000
African Others Sub 306 G=1.000 A=0.000, C=0.000
African American Sub 8042 G=1.0000 A=0.0000, C=0.0000
Asian Sub 168 G=1.000 A=0.000, C=0.000
East Asian Sub 112 G=1.000 A=0.000, C=0.000
Other Asian Sub 56 G=1.00 A=0.00, C=0.00
Latin American 1 Sub 500 G=1.000 A=0.000, C=0.000
Latin American 2 Sub 628 G=1.000 A=0.000, C=0.000
South Asian Sub 98 G=1.00 A=0.00, C=0.00
Other Sub 8298 G=1.0000 A=0.0000, C=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 G=0.999989 A=0.000011
Allele Frequency Aggregator Total Global 44420 G=0.99995 A=0.00005, C=0.00000
Allele Frequency Aggregator European Sub 32650 G=0.99994 A=0.00006, C=0.00000
Allele Frequency Aggregator Other Sub 6864 G=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator African Sub 3512 G=1.0000 A=0.0000, C=0.0000
Allele Frequency Aggregator Latin American 2 Sub 628 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Latin American 1 Sub 500 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator Asian Sub 168 G=1.000 A=0.000, C=0.000
Allele Frequency Aggregator South Asian Sub 98 G=1.00 A=0.00, C=0.00
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 5 NC_000005.10:g.161897258G>A
GRCh38.p14 chr 5 NC_000005.10:g.161897258G>C
GRCh37.p13 chr 5 NC_000005.9:g.161324264G>A
GRCh37.p13 chr 5 NC_000005.9:g.161324264G>C
GABRA1 RefSeqGene NG_011548.1:g.55068G>A
GABRA1 RefSeqGene NG_011548.1:g.55068G>C
Gene: GABRA1, gamma-aminobutyric acid type A receptor subunit alpha1 (plus strand)
Molecule type Change Amino acid[Codon] SO Term
GABRA1 transcript variant 1 NM_000806.5:c.1207G>A E [GAA] > K [AAA] Coding Sequence Variant
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_000797.2:p.Glu403Lys E (Glu) > K (Lys) Missense Variant
GABRA1 transcript variant 1 NM_000806.5:c.1207G>C E [GAA] > Q [CAA] Coding Sequence Variant
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_000797.2:p.Glu403Gln E (Glu) > Q (Gln) Missense Variant
GABRA1 transcript variant 3 NM_001127644.2:c.1207G>A E [GAA] > K [AAA] Coding Sequence Variant
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_001121116.1:p.Glu403Lys E (Glu) > K (Lys) Missense Variant
GABRA1 transcript variant 3 NM_001127644.2:c.1207G>C E [GAA] > Q [CAA] Coding Sequence Variant
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_001121116.1:p.Glu403Gln E (Glu) > Q (Gln) Missense Variant
GABRA1 transcript variant 7 NM_001127648.2:c.1207G>A E [GAA] > K [AAA] Coding Sequence Variant
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_001121120.1:p.Glu403Lys E (Glu) > K (Lys) Missense Variant
GABRA1 transcript variant 7 NM_001127648.2:c.1207G>C E [GAA] > Q [CAA] Coding Sequence Variant
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_001121120.1:p.Glu403Gln E (Glu) > Q (Gln) Missense Variant
GABRA1 transcript variant 2 NM_001127643.2:c.1207G>A E [GAA] > K [AAA] Coding Sequence Variant
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_001121115.1:p.Glu403Lys E (Glu) > K (Lys) Missense Variant
GABRA1 transcript variant 2 NM_001127643.2:c.1207G>C E [GAA] > Q [CAA] Coding Sequence Variant
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_001121115.1:p.Glu403Gln E (Glu) > Q (Gln) Missense Variant
GABRA1 transcript variant 4 NM_001127645.2:c.1207G>A E [GAA] > K [AAA] Coding Sequence Variant
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_001121117.1:p.Glu403Lys E (Glu) > K (Lys) Missense Variant
GABRA1 transcript variant 4 NM_001127645.2:c.1207G>C E [GAA] > Q [CAA] Coding Sequence Variant
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_001121117.1:p.Glu403Gln E (Glu) > Q (Gln) 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: 1401265 )
ClinVar Accession Disease Names Clinical Significance
RCV002025530.3 Epilepsy, childhood absence 4,Epilepsy, idiopathic generalized, susceptibility to, 13,Idiopathic generalized epilepsy Uncertain-Significance
Allele: C (allele ID: 406687 )
ClinVar Accession Disease Names Clinical Significance
RCV000484562.4 not provided Uncertain-Significance
RCV000824853.1 Developmental and epileptic encephalopathy, 19 Likely-Pathogenic
RCV000850482.1 Marfanoid habitus and intellectual disability Uncertain-Significance
RCV001213930.4 Epilepsy, childhood absence 4,Epilepsy, idiopathic generalized, susceptibility to, 13,Idiopathic generalized epilepsy 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 5 NC_000005.10:g.161897258= NC_000005.10:g.161897258G>A NC_000005.10:g.161897258G>C
GRCh37.p13 chr 5 NC_000005.9:g.161324264= NC_000005.9:g.161324264G>A NC_000005.9:g.161324264G>C
GABRA1 RefSeqGene NG_011548.1:g.55068= NG_011548.1:g.55068G>A NG_011548.1:g.55068G>C
GABRA1 transcript variant 1 NM_000806.5:c.1207= NM_000806.5:c.1207G>A NM_000806.5:c.1207G>C
GABRA1 transcript variant 3 NM_001127644.2:c.1207= NM_001127644.2:c.1207G>A NM_001127644.2:c.1207G>C
GABRA1 transcript variant 3 NM_001127644.1:c.1207= NM_001127644.1:c.1207G>A NM_001127644.1:c.1207G>C
GABRA1 transcript variant 2 NM_001127643.2:c.1207= NM_001127643.2:c.1207G>A NM_001127643.2:c.1207G>C
GABRA1 transcript variant 2 NM_001127643.1:c.1207= NM_001127643.1:c.1207G>A NM_001127643.1:c.1207G>C
GABRA1 transcript variant 7 NM_001127648.2:c.1207= NM_001127648.2:c.1207G>A NM_001127648.2:c.1207G>C
GABRA1 transcript variant 7 NM_001127648.1:c.1207= NM_001127648.1:c.1207G>A NM_001127648.1:c.1207G>C
GABRA1 transcript variant 4 NM_001127645.2:c.1207= NM_001127645.2:c.1207G>A NM_001127645.2:c.1207G>C
GABRA1 transcript variant 4 NM_001127645.1:c.1207= NM_001127645.1:c.1207G>A NM_001127645.1:c.1207G>C
GABRA1 transcript variant 6 NM_001127647.1:c.1207= NM_001127647.1:c.1207G>A NM_001127647.1:c.1207G>C
GABRA1 transcript variant 5 NM_001127646.1:c.1207= NM_001127646.1:c.1207G>A NM_001127646.1:c.1207G>C
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_000797.2:p.Glu403= NP_000797.2:p.Glu403Lys NP_000797.2:p.Glu403Gln
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_001121116.1:p.Glu403= NP_001121116.1:p.Glu403Lys NP_001121116.1:p.Glu403Gln
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_001121115.1:p.Glu403= NP_001121115.1:p.Glu403Lys NP_001121115.1:p.Glu403Gln
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_001121120.1:p.Glu403= NP_001121120.1:p.Glu403Lys NP_001121120.1:p.Glu403Gln
gamma-aminobutyric acid receptor subunit alpha-1 precursor NP_001121117.1:p.Glu403= NP_001121117.1:p.Glu403Lys NP_001121117.1:p.Glu403Gln
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#.

4 SubSNP, 6 Frequency, 5 ClinVar submissions
No Submitter Submission ID Date (Build)
1 EVA_EXAC ss1688072682 Apr 01, 2015 (144)
2 EVA_EXAC ss1688072683 Apr 01, 2015 (144)
3 GNOMAD ss2735405670 Nov 08, 2017 (151)
4 TOPMED ss4686096153 Apr 26, 2021 (155)
5 ExAC

Submission ignored due to conflicting rows:
Row 8084659 (NC_000005.9:161324263:G:G 121323/121324, NC_000005.9:161324263:G:A 1/121324)
Row 8084660 (NC_000005.9:161324263:G:G 121323/121324, NC_000005.9:161324263:G:C 1/121324)

- Oct 12, 2018 (152)
6 ExAC

Submission ignored due to conflicting rows:
Row 8084659 (NC_000005.9:161324263:G:G 121323/121324, NC_000005.9:161324263:G:A 1/121324)
Row 8084660 (NC_000005.9:161324263:G:G 121323/121324, NC_000005.9:161324263:G:C 1/121324)

- Oct 12, 2018 (152)
7 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 4539274 (NC_000005.9:161324263:G:G 251119/251120, NC_000005.9:161324263:G:A 1/251120)
Row 4539275 (NC_000005.9:161324263:G:G 251118/251120, NC_000005.9:161324263:G:C 2/251120)

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

Submission ignored due to conflicting rows:
Row 4539274 (NC_000005.9:161324263:G:G 251119/251120, NC_000005.9:161324263:G:A 1/251120)
Row 4539275 (NC_000005.9:161324263:G:G 251118/251120, NC_000005.9:161324263:G:C 2/251120)

- Jul 13, 2019 (153)
9 TopMed NC_000005.10 - 161897258 Apr 26, 2021 (155)
10 ALFA NC_000005.10 - 161897258 Apr 26, 2021 (155)
11 ClinVar RCV000484562.4 Oct 13, 2022 (156)
12 ClinVar RCV000824853.1 Apr 26, 2020 (154)
13 ClinVar RCV000850482.1 Apr 26, 2020 (154)
14 ClinVar RCV001213930.4 Oct 13, 2022 (156)
15 ClinVar RCV002025530.3 Oct 13, 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
ss1688072682, ss2735405670 NC_000005.9:161324263:G:A NC_000005.10:161897257:G:A (self)
RCV002025530.3, 523473710, 6182200360, ss4686096153 NC_000005.10:161897257:G:A NC_000005.10:161897257:G:A (self)
ss1688072683, ss2735405670 NC_000005.9:161324263:G:C NC_000005.10:161897257:G:C (self)
RCV000484562.4, RCV000824853.1, RCV000850482.1, RCV001213930.4, 6182200360 NC_000005.10:161897257:G:C NC_000005.10:161897257:G:C (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 rs775157869

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