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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 Aliases 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.

rs199561280

Current Build 153

Released July 9, 2019

Organism
Homo sapiens
Position
chr5:151822809 (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
C>A / C>T
Variation Type
SNV Single Nucleotide Variation
Frequency
T=0.00020 (25/125568, TOPMED)
T=0.0003 (20/78700, PAGE_STUDY)
T=0.0002 (6/31386, GnomAD) (+ 4 more)
T=0.0002 (3/13006, GO-ESP)
T=0.000 (1/5008, 1000G)
T=0.000 (0/3854, ALSPAC)
T=0.000 (1/3708, TWINSUK)
Clinical Significance
Reported in ClinVar
Gene : Consequence
GLRA1 : Missense Variant
Publications
0 citations
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 5 NC_000005.10:g.151822809C>A
GRCh38.p12 chr 5 NC_000005.10:g.151822809C>T
GRCh37.p13 chr 5 NC_000005.9:g.151202370C>A
GRCh37.p13 chr 5 NC_000005.9:g.151202370C>T
GLRA1 RefSeqGene NG_011764.1:g.107028G>T
GLRA1 RefSeqGene NG_011764.1:g.107028G>A
Gene: GLRA1, glycine receptor alpha 1 (minus strand)
Molecule type Change Amino acid[Codon] SO Term
GLRA1 transcript variant 1 NM_001146040.2:c.1238G>T R [CGA] > L [CTA] Coding Sequence Variant
glycine receptor subunit alpha-1 isoform 1 precursor NP_001139512.1:p.Arg413Leu R (Arg) > L (Leu) Missense Variant
GLRA1 transcript variant 1 NM_001146040.2:c.1238G>A R [CGA] > Q [CAA] Coding Sequence Variant
glycine receptor subunit alpha-1 isoform 1 precursor NP_001139512.1:p.Arg413Gln R (Arg) > Q (Gln) Missense Variant
GLRA1 transcript variant 2 NM_000171.4:c.1214G>T R [CGA] > L [CTA] Coding Sequence Variant
glycine receptor subunit alpha-1 isoform 2 precursor NP_000162.2:p.Arg405Leu R (Arg) > L (Leu) Missense Variant
GLRA1 transcript variant 2 NM_000171.4:c.1214G>A R [CGA] > Q [CAA] Coding Sequence Variant
glycine receptor subunit alpha-1 isoform 2 precursor NP_000162.2:p.Arg405Gln R (Arg) > Q (Gln) Missense Variant
GLRA1 transcript variant 3 NM_001292000.2:c.965G>T R [CGA] > L [CTA] Coding Sequence Variant
glycine receptor subunit alpha-1 isoform 3 NP_001278929.1:p.Arg322Leu R (Arg) > L (Leu) Missense Variant
GLRA1 transcript variant 3 NM_001292000.2:c.965G>A R [CGA] > Q [CAA] Coding Sequence Variant
glycine receptor subunit alpha-1 isoform 3 NP_001278929.1:p.Arg322Gln R (Arg) > 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: T (allele ID: 302516 )
ClinVar Accession Disease Names Clinical Significance
RCV000363497.1 Hyperekplexia Likely-Benign
RCV000560505.3 Hyperekplexia hereditary Uncertain-Significance
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
TopMed Global Study-wide 125568 C=0.99980 T=0.00020
The PAGE Study Global Study-wide 78700 C=0.9997 T=0.0003
The PAGE Study AfricanAmerican Sub 32514 C=1.0000 T=0.0000
The PAGE Study Mexican Sub 10810 C=0.9998 T=0.0002
The PAGE Study Asian Sub 8318 C=1.000 T=0.000
The PAGE Study PuertoRican Sub 7918 C=0.998 T=0.002
The PAGE Study NativeHawaiian Sub 4534 C=1.000 T=0.000
The PAGE Study Cuban Sub 4230 C=1.000 T=0.000
The PAGE Study Dominican Sub 3828 C=1.000 T=0.000
The PAGE Study CentralAmerican Sub 2450 C=1.000 T=0.000
The PAGE Study SouthAmerican Sub 1982 C=1.000 T=0.000
The PAGE Study NativeAmerican Sub 1260 C=1.000 T=0.000
The PAGE Study SouthAsian Sub 856 C=1.00 T=0.00
gnomAD - Genomes Global Study-wide 31386 C=0.9998 T=0.0002
gnomAD - Genomes European Sub 18900 C=0.9997 T=0.0003
gnomAD - Genomes African Sub 8702 C=1.000 T=0.000
gnomAD - Genomes East Asian Sub 1560 C=1.000 T=0.000
gnomAD - Genomes Other Sub 1086 C=1.000 T=0.000
gnomAD - Genomes American Sub 848 C=1.00 T=0.00
gnomAD - Genomes Ashkenazi Jewish Sub 290 C=1.00 T=0.00
GO Exome Sequencing Project Global Study-wide 13006 C=0.9998 T=0.0002
GO Exome Sequencing Project European American Sub 8600 C=1.000 T=0.000
GO Exome Sequencing Project African American Sub 4406 C=1.000 T=0.000
1000Genomes Global Study-wide 5008 C=1.000 T=0.000
1000Genomes African Sub 1322 C=1.000 T=0.000
1000Genomes East Asian Sub 1008 C=1.000 T=0.000
1000Genomes Europe Sub 1006 C=1.000 T=0.000
1000Genomes South Asian Sub 978 C=1.00 T=0.00
1000Genomes American Sub 694 C=1.00 T=0.00
The Avon Longitudinal Study of Parents and Children PARENT AND CHILD COHORT Study-wide 3854 C=1.000 T=0.000
UK 10K study - Twins TWIN COHORT Study-wide 3708 C=1.000 T=0.000
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 C= A T Note
GRCh38.p12 chr 5 NC_000005.10:g.15...

NC_000005.10:g.151822809=

NC_000005.10:g.15...

NC_000005.10:g.151822809C>A

NC_000005.10:g.15...

NC_000005.10:g.151822809C>T

GRCh37.p13 chr 5 NC_000005.9:g.151...

NC_000005.9:g.151202370=

NC_000005.9:g.151...

NC_000005.9:g.151202370C>A

NC_000005.9:g.151...

NC_000005.9:g.151202370C>T

GLRA1 RefSeqGene NG_011764.1:g.107...

NG_011764.1:g.107028=

NG_011764.1:g.107...

NG_011764.1:g.107028G>T

NG_011764.1:g.107...

NG_011764.1:g.107028G>A

GLRA1 transcript variant 2 NM_000171.4:c.1214= NM_000171.4:c.121...

NM_000171.4:c.1214G>T

NM_000171.4:c.121...

NM_000171.4:c.1214G>A

GLRA1 transcript variant 2 NM_000171.3:c.1214= NM_000171.3:c.121...

NM_000171.3:c.1214G>T

NM_000171.3:c.121...

NM_000171.3:c.1214G>A

GLRA1 transcript variant 1 NM_001146040.2:c....

NM_001146040.2:c.1238=

NM_001146040.2:c....

NM_001146040.2:c.1238G>T

NM_001146040.2:c....

NM_001146040.2:c.1238G>A

GLRA1 transcript variant 1 NM_001146040.1:c....

NM_001146040.1:c.1238=

NM_001146040.1:c....

NM_001146040.1:c.1238G>T

NM_001146040.1:c....

NM_001146040.1:c.1238G>A

GLRA1 transcript variant 3 NM_001292000.2:c....

NM_001292000.2:c.965=

NM_001292000.2:c....

NM_001292000.2:c.965G>T

NM_001292000.2:c....

NM_001292000.2:c.965G>A

GLRA1 transcript variant 3 NM_001292000.1:c....

NM_001292000.1:c.965=

NM_001292000.1:c....

NM_001292000.1:c.965G>T

NM_001292000.1:c....

NM_001292000.1:c.965G>A

glycine receptor subunit alpha-1 isoform 2 precursor NP_000162.2:p.Arg...

NP_000162.2:p.Arg405=

NP_000162.2:p.Arg...

NP_000162.2:p.Arg405Leu

NP_000162.2:p.Arg...

NP_000162.2:p.Arg405Gln

glycine receptor subunit alpha-1 isoform 1 precursor NP_001139512.1:p....

NP_001139512.1:p.Arg413=

NP_001139512.1:p....

NP_001139512.1:p.Arg413Leu

NP_001139512.1:p....

NP_001139512.1:p.Arg413Gln

glycine receptor subunit alpha-1 isoform 3 NP_001278929.1:p....

NP_001278929.1:p.Arg322=

NP_001278929.1:p....

NP_001278929.1:p.Arg322Leu

NP_001278929.1:p....

NP_001278929.1:p.Arg322Gln

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#.

36 SubSNP, 11 Frequency, 2 ClinVar submissions
No Submitter Submission ID Date (Build)
1 1000GENOMES ss488820861 May 04, 2012 (137)
2 EXOME_CHIP ss491374487 May 04, 2012 (137)
3 NHLBI-ESP ss712678035 Apr 25, 2013 (138)
4 ILLUMINA ss780843098 Sep 08, 2015 (146)
5 ILLUMINA ss783526505 Sep 08, 2015 (146)
6 1000GENOMES ss1317778854 Aug 21, 2014 (142)
7 EVA_DECODE ss1591800421 Apr 01, 2015 (144)
8 EVA_UK10K_ALSPAC ss1614315226 Apr 01, 2015 (144)
9 EVA_UK10K_TWINSUK ss1657309259 Apr 01, 2015 (144)
10 EVA_EXAC ss1688052961 Apr 01, 2015 (144)
11 EVA_EXAC ss1688052962 Apr 01, 2015 (144)
12 ILLUMINA ss1752557116 Sep 08, 2015 (146)
13 ILLUMINA ss1917796530 Feb 12, 2016 (147)
14 ILLUMINA ss1946160057 Feb 12, 2016 (147)
15 ILLUMINA ss1958835809 Feb 12, 2016 (147)
16 HUMAN_LONGEVITY ss2279333149 Dec 20, 2016 (150)
17 TOPMED ss2447652112 Dec 20, 2016 (150)
18 GNOMAD ss2735375788 Nov 08, 2017 (151)
19 GNOMAD ss2747495690 Nov 08, 2017 (151)
20 GNOMAD ss2832383505 Nov 08, 2017 (151)
21 AFFY ss2985342334 Nov 08, 2017 (151)
22 AFFY ss2985972111 Nov 08, 2017 (151)
23 ILLUMINA ss3022544117 Nov 08, 2017 (151)
24 TOPMED ss3482366105 Nov 08, 2017 (151)
25 ILLUMINA ss3629374206 Oct 12, 2018 (152)
26 ILLUMINA ss3635029771 Oct 12, 2018 (152)
27 ILLUMINA ss3640737065 Oct 12, 2018 (152)
28 ILLUMINA ss3644893071 Oct 12, 2018 (152)
29 ILLUMINA ss3653048569 Oct 12, 2018 (152)
30 ILLUMINA ss3654112671 Oct 12, 2018 (152)
31 EVA_DECODE ss3715973947 Jul 13, 2019 (153)
32 ILLUMINA ss3726283549 Jul 13, 2019 (153)
33 ILLUMINA ss3744542746 Jul 13, 2019 (153)
34 ILLUMINA ss3745329948 Jul 13, 2019 (153)
35 PAGE_CC ss3771241446 Jul 13, 2019 (153)
36 ILLUMINA ss3772823865 Jul 13, 2019 (153)
37 1000Genomes NC_000005.9 - 151202370 Oct 12, 2018 (152)
38 The Avon Longitudinal Study of Parents and Children NC_000005.9 - 151202370 Oct 12, 2018 (152)
39 ExAC

Submission ignored due to conflicting rows:
Row 8063487 (NC_000005.9:151202369:C:C 121393/121394, NC_000005.9:151202369:C:A 1/121394)
Row 8063488 (NC_000005.9:151202369:C:C 121360/121394, NC_000005.9:151202369:C:T 34/121394)

- Oct 12, 2018 (152)
40 ExAC

Submission ignored due to conflicting rows:
Row 8063487 (NC_000005.9:151202369:C:C 121393/121394, NC_000005.9:151202369:C:A 1/121394)
Row 8063488 (NC_000005.9:151202369:C:C 121360/121394, NC_000005.9:151202369:C:T 34/121394)

- Oct 12, 2018 (152)
41 gnomAD - Genomes NC_000005.9 - 151202370 Jul 13, 2019 (153)
42 gnomAD - Exomes

Submission ignored due to conflicting rows:
Row 4508318 (NC_000005.9:151202369:C:C 251395/251396, NC_000005.9:151202369:C:A 1/251396)
Row 4508319 (NC_000005.9:151202369:C:C 251326/251396, NC_000005.9:151202369:C:T 70/251396)

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

Submission ignored due to conflicting rows:
Row 4508318 (NC_000005.9:151202369:C:C 251395/251396, NC_000005.9:151202369:C:A 1/251396)
Row 4508319 (NC_000005.9:151202369:C:C 251326/251396, NC_000005.9:151202369:C:T 70/251396)

- Jul 13, 2019 (153)
44 GO Exome Sequencing Project NC_000005.9 - 151202370 Oct 12, 2018 (152)
45 The PAGE Study NC_000005.10 - 151822809 Jul 13, 2019 (153)
46 TopMed NC_000005.10 - 151822809 Oct 12, 2018 (152)
47 UK 10K study - Twins NC_000005.9 - 151202370 Oct 12, 2018 (152)
48 ClinVar RCV000363497.1 Oct 12, 2018 (152)
49 ClinVar RCV000560505.3 Jul 13, 2019 (153)
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
ss1688052962, ss2735375788 NC_000005.9:151202369:C:A NC_000005.10:151822808:C:A (self)
ss1591800421 NC_000005.8:151182562:C:T NC_000005.10:151822808:C:T (self)
29477404, 16403319, 80653254, 591118, 16403319, ss488820861, ss491374487, ss712678035, ss780843098, ss783526505, ss1317778854, ss1614315226, ss1657309259, ss1688052961, ss1752557116, ss1917796530, ss1946160057, ss1958835809, ss2447652112, ss2735375788, ss2747495690, ss2832383505, ss2985342334, ss2985972111, ss3022544117, ss3629374206, ss3635029771, ss3640737065, ss3644893071, ss3653048569, ss3654112671, ss3744542746, ss3745329948, ss3772823865 NC_000005.9:151202369:C:T NC_000005.10:151822808:C:T (self)
RCV000363497.1, RCV000560505.3, 462915, 325788289, ss2279333149, ss3482366105, ss3715973947, ss3726283549, ss3771241446 NC_000005.10:151822808:C:T NC_000005.10:151822808:C:T (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 rs199561280

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.post308+0fe9b3b