rs376029542
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 3P and 11B. PM1PP2BP4_ModerateBP6BS1BS2
The NM_001134407.3(GRIN2A):c.2165C>T(p.Thr722Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000601 in 1,613,774 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). Synonymous variant affecting the same amino acid position (i.e. T722T) has been classified as Likely benign.
Frequency
Consequence
NM_001134407.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRIN2A | NM_001134407.3 | c.2165C>T | p.Thr722Met | missense_variant | 10/13 | ENST00000330684.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRIN2A | ENST00000330684.4 | c.2165C>T | p.Thr722Met | missense_variant | 10/13 | 1 | NM_001134407.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000237 AC: 36AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000115 AC: 29AN: 251176Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135756
GnomAD4 exome AF: 0.0000424 AC: 62AN: 1461514Hom.: 0 Cov.: 31 AF XY: 0.0000385 AC XY: 28AN XY: 727070
GnomAD4 genome AF: 0.000230 AC: 35AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74440
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | May 11, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 12, 2021 | This variant is associated with the following publications: (PMID: 28166811, 27839871, 30919572) - |
Landau-Kleffner syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 02, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 05, 2022 | 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