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
Consequence
ENST00000274576.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GLRA1 | NM_000171.4 | c.1108G>A | p.Gly370Ser | missense_variant | 9/9 | ENST00000274576.9 | NP_000162.2 | |
GLRA1 | NM_001146040.2 | c.1132G>A | p.Gly378Ser | missense_variant | 9/9 | NP_001139512.1 | ||
GLRA1 | NM_001292000.2 | c.859G>A | p.Gly287Ser | missense_variant | 8/8 | NP_001278929.1 | ||
GLRA1 | XM_047417105.1 | c.1156G>A | p.Gly386Ser | missense_variant | 9/9 | XP_047273061.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GLRA1 | ENST00000274576.9 | c.1108G>A | p.Gly370Ser | missense_variant | 9/9 | 1 | NM_000171.4 | ENSP00000274576 | P4 | |
GLRA1 | ENST00000455880.2 | c.1132G>A | p.Gly378Ser | missense_variant | 9/9 | 1 | ENSP00000411593 | A1 | ||
GLRA1 | ENST00000462581.6 | c.*866G>A | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 | 1 | ENSP00000430595 |
Frequencies
GnomAD3 genomes AF: 0.00933 AC: 1419AN: 152124Hom.: 7 Cov.: 31
GnomAD3 exomes AF: 0.00962 AC: 2412AN: 250714Hom.: 20 AF XY: 0.00972 AC XY: 1316AN XY: 135442
GnomAD4 exome AF: 0.0127 AC: 18541AN: 1461192Hom.: 130 Cov.: 32 AF XY: 0.0125 AC XY: 9074AN XY: 726808
GnomAD4 genome AF: 0.00932 AC: 1419AN: 152242Hom.: 7 Cov.: 31 AF XY: 0.00928 AC XY: 691AN XY: 74426
ClinVar
Submissions by phenotype
Hyperekplexia 1 Pathogenic:1Benign:6
Benign, criteria provided, single submitter | clinical testing | Molecular Genetics, Royal Melbourne Hospital | May 04, 2023 | European 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 submission | curation | GeneReviews | Oct 04, 2012 | - - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | This 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 submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Likely benign, criteria provided, single submitter | research | Broad 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 submitter | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | Oct 09, 2014 | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 22, 2019 | This variant is associated with the following publications: (PMID: 27535533, 26764160, 27884173, 10817489, 20981092, 25333069, 20631190) - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
GLRA1-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 05, 2019 | This 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 submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 28, 2016 | Variant 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 submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Feb 01, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at