19-41999108-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP7
The NM_002088.5(GRIK5):c.2706G>A(p.Ala902Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000082 in 1,219,542 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. A902A) has been classified as Likely benign.
Frequency
Consequence
NM_002088.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRIK5 | ENST00000593562.6 | c.2706G>A | p.Ala902Ala | synonymous_variant | Exon 20 of 20 | 5 | NM_002088.5 | ENSP00000470251.1 | ||
GRIK5 | ENST00000262895.7 | c.2706G>A | p.Ala902Ala | synonymous_variant | Exon 19 of 19 | 1 | ENSP00000262895.2 | |||
GRIK5 | ENST00000454993.6 | n.1583G>A | non_coding_transcript_exon_variant | Exon 9 of 9 | 1 | |||||
GRIK5 | ENST00000602210.1 | n.*135G>A | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 8.20e-7 AC: 1AN: 1219542Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 596962
GnomAD4 genome Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at