rs373321710
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP2BP4_Strong
The NM_001278064.2(GRM1):c.3328G>A(p.Val1110Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,614,012 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001278064.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRM1 | NM_001278064.2 | c.3328G>A | p.Val1110Met | missense_variant | 8/8 | ENST00000282753.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRM1 | ENST00000282753.6 | c.3328G>A | p.Val1110Met | missense_variant | 8/8 | 1 | NM_001278064.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250666Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135658
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461846Hom.: 0 Cov.: 60 AF XY: 0.00000825 AC XY: 6AN XY: 727226
GnomAD4 genome ? AF: 0.0000920 AC: 14AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74334
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Aug 22, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at