16-9763339-C-T
Variant summary
Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS1
The NM_001134407.3(GRIN2A):c.4205G>A(p.Arg1402Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000805 in 1,614,068 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 (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1402P) has been classified as Likely benign.
Frequency
Consequence
NM_001134407.3 missense
Scores
Clinical Significance
Conservation
Publications
- complex neurodevelopmental disorderInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- Landau-Kleffner syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- continuous spikes and waves during sleepInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- early-onset epileptic encephalopathy and intellectual disability due to GRIN2A mutationInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- rolandic epilepsy-speech dyspraxia syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- self-limited epilepsy with centrotemporal spikesInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- neurodevelopmental disorderInheritance: AR Classification: LIMITED Submitted by: G2P
Genome browser will be placed here
ACMG classification
Our verdict: Benign. The variant received -14 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152090Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000318 AC: 8AN: 251186 AF XY: 0.0000221 show subpopulations
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461860Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727236 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152208Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74414 show subpopulations
ClinVar
Submissions by phenotype
not provided Benign:2
GRIN2A: BP4 -
- -
Landau-Kleffner syndrome Benign:1
- -
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. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at