11-88508867-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001143831.3(GRM5):c.3364G>A(p.Glu1122Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000208 in 1,583,768 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_001143831.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRM5 | ENST00000305447.5 | c.3364G>A | p.Glu1122Lys | missense_variant | Exon 10 of 10 | 1 | NM_001143831.3 | ENSP00000306138.4 | ||
GRM5 | ENST00000305432.9 | c.3268G>A | p.Glu1090Lys | missense_variant | Exon 8 of 8 | 1 | ENSP00000305905.5 | |||
GRM5 | ENST00000455756.6 | c.3268G>A | p.Glu1090Lys | missense_variant | Exon 9 of 9 | 2 | ENSP00000405690.2 | |||
GRM5-AS1 | ENST00000526448.1 | n.4292C>T | non_coding_transcript_exon_variant | Exon 1 of 6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000987 AC: 15AN: 151980Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000400 AC: 8AN: 200184Hom.: 0 AF XY: 0.0000365 AC XY: 4AN XY: 109502
GnomAD4 exome AF: 0.000219 AC: 314AN: 1431788Hom.: 0 Cov.: 34 AF XY: 0.000206 AC XY: 146AN XY: 710286
GnomAD4 genome AF: 0.0000987 AC: 15AN: 151980Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74226
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3364G>A (p.E1122K) 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 3364, causing the glutamic acid (E) at amino acid position 1122 to be replaced by a lysine (K). 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