11-88508809-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001143831.3(GRM5):c.3422G>A(p.Arg1141Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000164 in 1,521,852 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001143831.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRM5 | ENST00000305447.5 | c.3422G>A | p.Arg1141Gln | missense_variant | Exon 10 of 10 | 1 | NM_001143831.3 | ENSP00000306138.4 | ||
GRM5 | ENST00000305432.9 | c.3326G>A | p.Arg1109Gln | missense_variant | Exon 8 of 8 | 1 | ENSP00000305905.5 | |||
GRM5 | ENST00000455756.6 | c.3326G>A | p.Arg1109Gln | missense_variant | Exon 9 of 9 | 2 | ENSP00000405690.2 | |||
GRM5-AS1 | ENST00000526448.1 | n.4234C>T | non_coding_transcript_exon_variant | Exon 1 of 6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 151874Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000864 AC: 10AN: 115676Hom.: 0 AF XY: 0.0000939 AC XY: 6AN XY: 63918
GnomAD4 exome AF: 0.000166 AC: 228AN: 1369978Hom.: 0 Cov.: 30 AF XY: 0.000172 AC XY: 116AN XY: 675456
GnomAD4 genome AF: 0.000145 AC: 22AN: 151874Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74172
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3422G>A (p.R1141Q) alteration is located in exon 9 (coding exon 9) of the GRM5 gene. This alteration results from a G to A substitution at nucleotide position 3422, causing the arginine (R) at amino acid position 1141 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