rs149023945
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000171.4(GLRA1):āc.117G>Cā(p.Ser39=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00177 in 1,613,946 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. S39S) 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 -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRA1 | NM_000171.4 | c.117G>C | p.Ser39= | synonymous_variant | 2/9 | ENST00000274576.9 | |
GLRA1 | NM_001146040.2 | c.117G>C | p.Ser39= | synonymous_variant | 2/9 | ||
GLRA1 | XM_047417105.1 | c.165G>C | p.Ser55= | synonymous_variant | 2/9 | ||
GLRA1 | NM_001292000.2 | c.-65-5590G>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRA1 | ENST00000274576.9 | c.117G>C | p.Ser39= | synonymous_variant | 2/9 | 1 | NM_000171.4 | P4 | |
GLRA1 | ENST00000455880.2 | c.117G>C | p.Ser39= | synonymous_variant | 2/9 | 1 | A1 | ||
GLRA1 | ENST00000471351.2 | n.400G>C | non_coding_transcript_exon_variant | 2/8 | 1 | ||||
GLRA1 | ENST00000462581.6 | c.57-5590G>C | intron_variant, NMD_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00165 AC: 251AN: 152110Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00148 AC: 373AN: 251252Hom.: 1 AF XY: 0.00162 AC XY: 220AN XY: 135796
GnomAD4 exome AF: 0.00178 AC: 2601AN: 1461718Hom.: 2 Cov.: 31 AF XY: 0.00185 AC XY: 1344AN XY: 727174
GnomAD4 genome ? AF: 0.00166 AC: 253AN: 152228Hom.: 1 Cov.: 32 AF XY: 0.00161 AC XY: 120AN XY: 74416
ClinVar
Submissions by phenotype
Hyperekplexia 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 07, 2021 | - - |
Hereditary hyperekplexia Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at