chr5-151822730-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_000171.4(GLRA1):c.1293C>T(p.Asn431=) variant causes a synonymous change. The variant allele was found at a frequency of 0.00000958 in 1,461,576 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000096 ( 0 hom. )
Consequence
GLRA1
NM_000171.4 synonymous
NM_000171.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 5.71
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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
?
Variant 5-151822730-G-A is Benign according to our data. Variant chr5-151822730-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1109235.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRA1 | NM_000171.4 | c.1293C>T | p.Asn431= | synonymous_variant | 9/9 | ENST00000274576.9 | |
GLRA1 | NM_001146040.2 | c.1317C>T | p.Asn439= | synonymous_variant | 9/9 | ||
GLRA1 | NM_001292000.2 | c.1044C>T | p.Asn348= | synonymous_variant | 8/8 | ||
GLRA1 | XM_047417105.1 | c.1341C>T | p.Asn447= | synonymous_variant | 9/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRA1 | ENST00000274576.9 | c.1293C>T | p.Asn431= | synonymous_variant | 9/9 | 1 | NM_000171.4 | P4 | |
GLRA1 | ENST00000455880.2 | c.1317C>T | p.Asn439= | synonymous_variant | 9/9 | 1 | A1 | ||
GLRA1 | ENST00000462581.6 | c.*1051C>T | 3_prime_UTR_variant, NMD_transcript_variant | 8/8 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461576Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727120
GnomAD4 exome
AF:
AC:
14
AN:
1461576
Hom.:
Cov.:
31
AF XY:
AC XY:
6
AN XY:
727120
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hereditary hyperekplexia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 29, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at