rs192326771
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000171.4(GLRA1):c.888C>T(p.Ser296=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,374 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 (★★). Synonymous variant affecting the same amino acid position (i.e. S296S) has been classified as Likely benign.
Frequency
Consequence
NM_000171.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRA1 | NM_000171.4 | c.888C>T | p.Ser296= | synonymous_variant | 7/9 | ENST00000274576.9 | |
GLRA1 | NM_001146040.2 | c.888C>T | p.Ser296= | synonymous_variant | 7/9 | ||
GLRA1 | NM_001292000.2 | c.639C>T | p.Ser213= | synonymous_variant | 6/8 | ||
GLRA1 | XM_047417105.1 | c.936C>T | p.Ser312= | synonymous_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRA1 | ENST00000274576.9 | c.888C>T | p.Ser296= | synonymous_variant | 7/9 | 1 | NM_000171.4 | P4 | |
GLRA1 | ENST00000455880.2 | c.888C>T | p.Ser296= | synonymous_variant | 7/9 | 1 | A1 | ||
GLRA1 | ENST00000471351.2 | n.1171C>T | non_coding_transcript_exon_variant | 7/8 | 1 | ||||
GLRA1 | ENST00000462581.6 | c.*646C>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251422Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135884
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461102Hom.: 0 Cov.: 31 AF XY: 0.0000261 AC XY: 19AN XY: 726946
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152272Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74450
ClinVar
Submissions by phenotype
GLRA1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 30, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Hereditary hyperekplexia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 07, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at