X-14532285-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM1BP4_Moderate
The NM_002063.4(GLRA2):c.115T>C(p.Ser39Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000252 in 1,189,077 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002063.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRA2 | NM_002063.4 | c.115T>C | p.Ser39Pro | missense_variant | 2/9 | ENST00000218075.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRA2 | ENST00000218075.9 | c.115T>C | p.Ser39Pro | missense_variant | 2/9 | 1 | NM_002063.4 | A1 | |
GLRA2 | ENST00000355020.9 | c.115T>C | p.Ser39Pro | missense_variant | 2/9 | 1 | P4 | ||
GLRA2 | ENST00000415367.2 | n.366T>C | non_coding_transcript_exon_variant | 2/9 | 3 | ||||
GLRA2 | ENST00000443437.6 | c.*82T>C | 3_prime_UTR_variant, NMD_transcript_variant | 4/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000895 AC: 1AN: 111770Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1AN XY: 33990
GnomAD4 exome AF: 0.00000186 AC: 2AN: 1077307Hom.: 0 Cov.: 23 AF XY: 0.00000290 AC XY: 1AN XY: 344715
GnomAD4 genome ? AF: 0.00000895 AC: 1AN: 111770Hom.: 0 Cov.: 23 AF XY: 0.0000294 AC XY: 1AN XY: 33990
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.115T>C (p.S39P) alteration is located in exon 2 (coding exon 2) of the GLRA2 gene. This alteration results from a T to C substitution at nucleotide position 115, causing the serine (S) at amino acid position 39 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at