10-85602550-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_017551.3(GRID1):c.2753G>A(p.Arg918Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000198 in 1,613,882 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 Uncertain significance (★).
Frequency
Consequence
NM_017551.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRID1 | NM_017551.3 | c.2753G>A | p.Arg918Gln | missense_variant | Exon 16 of 16 | ENST00000327946.12 | NP_060021.1 | |
GRID1 | XM_047425122.1 | c.1466G>A | p.Arg489Gln | missense_variant | Exon 9 of 9 | XP_047281078.1 | ||
GRID1 | XM_047425123.1 | c.1466G>A | p.Arg489Gln | missense_variant | Exon 9 of 9 | XP_047281079.1 | ||
GRID1-AS1 | NR_038986.1 | n.282-2845C>T | intron_variant | Intron 2 of 2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152020Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000757 AC: 19AN: 251050Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135766
GnomAD4 exome AF: 0.000213 AC: 311AN: 1461862Hom.: 0 Cov.: 33 AF XY: 0.000209 AC XY: 152AN XY: 727224
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152020Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74228
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2753G>A (p.R918Q) alteration is located in exon 16 (coding exon 16) of the GRID1 gene. This alteration results from a G to A substitution at nucleotide position 2753, causing the arginine (R) at amino acid position 918 to be replaced by a glutamine (Q). 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