rs116474260

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000274576.9(GLRA1):​c.1108G>A​(p.Gly370Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0124 in 1,613,434 control chromosomes in the GnomAD database, including 137 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. G370G) has been classified as Likely benign.

Frequency

Genomes: 𝑓 0.0093 ( 7 hom., cov: 31)
Exomes 𝑓: 0.013 ( 130 hom. )

Consequence

GLRA1
ENST00000274576.9 missense

Scores

1
3
13

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts P:1B:11

Conservation

PhyloP100: 3.92
Variant links:
Genes affected
GLRA1 (HGNC:4326): (glycine receptor alpha 1) The protein encoded by this gene is a subunit of a pentameric inhibitory glycine receptor, which mediates postsynaptic inhibition in the central nervous system. Defects in this gene are a cause of startle disease (STHE), also known as hereditary hyperekplexia or congenital stiff-person syndrome. Multiple transcript variants encoding different isoforms have been found. [provided by RefSeq, Dec 2015]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.00745064).
BP6
Variant 5-151822915-C-T is Benign according to our data. Variant chr5-151822915-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 38327.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-151822915-C-T is described in Lovd as [Benign].
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00932 (1419/152242) while in subpopulation NFE AF= 0.0148 (1007/68012). AF 95% confidence interval is 0.014. There are 7 homozygotes in gnomad4. There are 691 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 7 AD,AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
GLRA1NM_000171.4 linkuse as main transcriptc.1108G>A p.Gly370Ser missense_variant 9/9 ENST00000274576.9 NP_000162.2
GLRA1NM_001146040.2 linkuse as main transcriptc.1132G>A p.Gly378Ser missense_variant 9/9 NP_001139512.1
GLRA1NM_001292000.2 linkuse as main transcriptc.859G>A p.Gly287Ser missense_variant 8/8 NP_001278929.1
GLRA1XM_047417105.1 linkuse as main transcriptc.1156G>A p.Gly386Ser missense_variant 9/9 XP_047273061.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
GLRA1ENST00000274576.9 linkuse as main transcriptc.1108G>A p.Gly370Ser missense_variant 9/91 NM_000171.4 ENSP00000274576 P4P23415-2
GLRA1ENST00000455880.2 linkuse as main transcriptc.1132G>A p.Gly378Ser missense_variant 9/91 ENSP00000411593 A1P23415-1
GLRA1ENST00000462581.6 linkuse as main transcriptc.*866G>A 3_prime_UTR_variant, NMD_transcript_variant 8/81 ENSP00000430595

Frequencies

GnomAD3 genomes
AF:
0.00933
AC:
1419
AN:
152124
Hom.:
7
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.00246
Gnomad AMI
AF:
0.0373
Gnomad AMR
AF:
0.00864
Gnomad ASJ
AF:
0.00605
Gnomad EAS
AF:
0.000193
Gnomad SAS
AF:
0.00580
Gnomad FIN
AF:
0.00565
Gnomad MID
AF:
0.00949
Gnomad NFE
AF:
0.0148
Gnomad OTH
AF:
0.0144
GnomAD3 exomes
AF:
0.00962
AC:
2412
AN:
250714
Hom.:
20
AF XY:
0.00972
AC XY:
1316
AN XY:
135442
show subpopulations
Gnomad AFR exome
AF:
0.00222
Gnomad AMR exome
AF:
0.00553
Gnomad ASJ exome
AF:
0.00889
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00526
Gnomad FIN exome
AF:
0.00598
Gnomad NFE exome
AF:
0.0153
Gnomad OTH exome
AF:
0.0115
GnomAD4 exome
AF:
0.0127
AC:
18541
AN:
1461192
Hom.:
130
Cov.:
32
AF XY:
0.0125
AC XY:
9074
AN XY:
726808
show subpopulations
Gnomad4 AFR exome
AF:
0.00260
Gnomad4 AMR exome
AF:
0.00595
Gnomad4 ASJ exome
AF:
0.00847
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.00521
Gnomad4 FIN exome
AF:
0.00573
Gnomad4 NFE exome
AF:
0.0147
Gnomad4 OTH exome
AF:
0.0114
GnomAD4 genome
AF:
0.00932
AC:
1419
AN:
152242
Hom.:
7
Cov.:
31
AF XY:
0.00928
AC XY:
691
AN XY:
74426
show subpopulations
Gnomad4 AFR
AF:
0.00246
Gnomad4 AMR
AF:
0.00863
Gnomad4 ASJ
AF:
0.00605
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00601
Gnomad4 FIN
AF:
0.00565
Gnomad4 NFE
AF:
0.0148
Gnomad4 OTH
AF:
0.0142
Alfa
AF:
0.0140
Hom.:
38
Bravo
AF:
0.00922
TwinsUK
AF:
0.0127
AC:
47
ALSPAC
AF:
0.00986
AC:
38
ESP6500AA
AF:
0.00477
AC:
21
ESP6500EA
AF:
0.0147
AC:
126
ExAC
AF:
0.0100
AC:
1214
Asia WGS
AF:
0.00462
AC:
16
AN:
3478
EpiCase
AF:
0.0155
EpiControl
AF:
0.0160

ClinVar

Significance: Benign/Likely benign
Submissions summary: Pathogenic:1Benign:11
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Hyperekplexia 1 Pathogenic:1Benign:6
Benign, criteria provided, single submitterclinical testingMolecular Genetics, Royal Melbourne HospitalMay 04, 2023European Non-Finnish population allele frequency is 1.473% (rs116474260, 1959/128696 alleles, 15 homozygotes in gnomAD v2.1). Based on the classification scheme RMH Modified ACMG/AMP Guidelines v1.5.1, this variant is classified as BENIGN. Following criteria are met: BA1 -
Pathogenic, flagged submissioncurationGeneReviewsOct 04, 2012- -
Benign, no assertion criteria providedclinical testingDiagnostic Laboratory, Department of Genetics, University Medical Center Groningen-- -
Likely benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaApr 27, 2017This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Likely benign, criteria provided, single submitterclinical testingMendelicsMay 28, 2019- -
Likely benign, criteria provided, single submitterresearchBroad Center for Mendelian Genomics, Broad Institute of MIT and Harvard-The heterozygous p.Gly370Ser variant, sometimes called p.Gly342Ser or p.Gly378Ser due to a difference in cDNA numbering, in GLRA1 has been identified in an individual with hyperekplexia and their unaffected parent (PMID: 10817489). This variant has also been identified in >1% of European (non-Finnish) chromosomes and 7 homozygotes by ExAC (http://gnomad.broadinstitute.org/). In vitro functional studies provide some evidence that the p.Gly370Ser variant may not impact protein function (PMID: 10817489). However, these types of assays may not accurately represent biological function. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely benign for hyperekplexia. -
Benign, criteria provided, single submitterclinical testingGenome Diagnostics Laboratory, University Medical Center UtrechtOct 09, 2014- -
not provided Benign:2
Benign, criteria provided, single submitterclinical testingGeneDxOct 22, 2019This variant is associated with the following publications: (PMID: 27535533, 26764160, 27884173, 10817489, 20981092, 25333069, 20631190) -
Likely benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
GLRA1-related disorder Benign:1
Benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesMar 05, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not specified Benign:1
Likely benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMar 28, 2016Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: DM? in HGMD, frequency -
Hereditary hyperekplexia Benign:1
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.18
BayesDel_addAF
Benign
-0.41
T
BayesDel_noAF
Benign
-0.35
CADD
Uncertain
24
DANN
Uncertain
0.99
Eigen
Benign
-0.25
Eigen_PC
Benign
-0.075
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Uncertain
0.92
D;D
MetaRNN
Benign
0.0075
T;T
MetaSVM
Benign
-0.53
T
MutationAssessor
Benign
1.9
.;L
MutationTaster
Benign
1.0
A;A;A
PrimateAI
Pathogenic
0.82
D
PROVEAN
Benign
-0.93
N;N
REVEL
Benign
0.24
Sift
Benign
0.11
T;T
Sift4G
Benign
0.35
T;T
Polyphen
0.0
B;B
Vest4
0.25
MVP
0.77
MPC
0.050
ClinPred
0.015
T
GERP RS
4.2
Varity_R
0.21
gMVP
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs116474260; hg19: chr5-151202476; API