12-13753515-G-A
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBS1BS2
The NM_000834.5(GRIN2B):c.812C>T(p.Ala271Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000905 in 1,614,098 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 Likely benign (★★).
Frequency
Consequence
NM_000834.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRIN2B | NM_000834.5 | c.812C>T | p.Ala271Val | missense_variant | Exon 4 of 14 | ENST00000609686.4 | NP_000825.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRIN2B | ENST00000609686.4 | c.812C>T | p.Ala271Val | missense_variant | Exon 4 of 14 | 1 | NM_000834.5 | ENSP00000477455.1 | ||
GRIN2B | ENST00000630791.2 | c.812C>T | p.Ala271Val | missense_variant | Exon 5 of 8 | 5 | ENSP00000486677.3 |
Frequencies
GnomAD3 genomes AF: 0.000519 AC: 79AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000163 AC: 41AN: 250910Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135620
GnomAD4 exome AF: 0.0000458 AC: 67AN: 1461822Hom.: 0 Cov.: 32 AF XY: 0.0000399 AC XY: 29AN XY: 727214
GnomAD4 genome AF: 0.000519 AC: 79AN: 152276Hom.: 0 Cov.: 33 AF XY: 0.000416 AC XY: 31AN XY: 74460
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Intellectual disability, autosomal dominant 6;C4015316:Developmental and epileptic encephalopathy, 27 Benign:1
- -
GRIN2B-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
This variant is associated with the following publications: (PMID: 24272827, 27818011) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at