chr19-1003374-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138690.3(GRIN3B):c.671C>T(p.Ala224Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000318 in 1,570,150 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A224G) has been classified as Uncertain significance.
Frequency
Consequence
NM_138690.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIN3B | NM_138690.3 | c.671C>T | p.Ala224Val | missense_variant | 2/9 | ENST00000234389.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIN3B | ENST00000234389.3 | c.671C>T | p.Ala224Val | missense_variant | 2/9 | 1 | NM_138690.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152202Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000659 AC: 11AN: 166988Hom.: 0 AF XY: 0.0000541 AC XY: 5AN XY: 92352
GnomAD4 exome AF: 0.0000289 AC: 41AN: 1417948Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 19AN XY: 702530
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152202Hom.: 0 Cov.: 34 AF XY: 0.0000404 AC XY: 3AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2022 | The c.671C>T (p.A224V) alteration is located in exon 2 (coding exon 2) of the GRIN3B gene. This alteration results from a C to T substitution at nucleotide position 671, causing the alanine (A) at amino acid position 224 to be replaced by a valine (V). 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