rs140672142
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBP6BS1
The NM_007327.4(GRIN1):c.1012G>A(p.Val338Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000366 in 1,613,456 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V338L) has been classified as Likely benign.
Frequency
Consequence
NM_007327.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIN1 | NM_007327.4 | c.1012G>A | p.Val338Met | missense_variant | 7/20 | ENST00000371561.8 | |
LOC105376328 | XR_007061876.1 | n.1507C>T | non_coding_transcript_exon_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIN1 | ENST00000371561.8 | c.1012G>A | p.Val338Met | missense_variant | 7/20 | 1 | NM_007327.4 |
Frequencies
GnomAD3 genomes ? AF: 0.000138 AC: 21AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250896Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135876
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461266Hom.: 0 Cov.: 33 AF XY: 0.0000248 AC XY: 18AN XY: 726926
GnomAD4 genome ? AF: 0.000138 AC: 21AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74346
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Oct 28, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 09, 2020 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 28, 2016 | The p.V338M variant (also known as c.1012G>A), located in coding exon 7 of the GRIN1 gene, results from a G to A substitution at nucleotide position 1012. The valine at codon 338 is replaced by methionine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Intellectual disability, autosomal dominant 8 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 25, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at