chrX-123184599-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_000828.5(GRIA3):c.64C>T(p.Leu22Phe) variant causes a missense change. The variant allele was found at a frequency of 0.0000116 in 1,206,288 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 Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L22I) has been classified as Uncertain significance.
Frequency
Consequence
NM_000828.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIA3 | NM_000828.5 | c.64C>T | p.Leu22Phe | missense_variant | 1/16 | ENST00000622768.5 | |
GRIA3 | NM_007325.5 | c.64C>T | p.Leu22Phe | missense_variant | 1/16 | ENST00000620443.2 | |
GRIA3 | NM_001256743.2 | c.64C>T | p.Leu22Phe | missense_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIA3 | ENST00000620443.2 | c.64C>T | p.Leu22Phe | missense_variant | 1/16 | 1 | NM_007325.5 | P4 | |
GRIA3 | ENST00000622768.5 | c.64C>T | p.Leu22Phe | missense_variant | 1/16 | 5 | NM_000828.5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000271 AC: 3AN: 110604Hom.: 0 Cov.: 21 AF XY: 0.0000305 AC XY: 1AN XY: 32828
GnomAD3 exomes AF: 0.0000382 AC: 7AN: 183412Hom.: 0 AF XY: 0.0000295 AC XY: 2AN XY: 67846
GnomAD4 exome AF: 0.0000100 AC: 11AN: 1095636Hom.: 0 Cov.: 29 AF XY: 0.00000277 AC XY: 1AN XY: 361060
GnomAD4 genome ? AF: 0.0000271 AC: 3AN: 110652Hom.: 0 Cov.: 21 AF XY: 0.0000304 AC XY: 1AN XY: 32886
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 18, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at