rs764292783
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2BP4_ModerateBP6BS2
The NM_001134407.3(GRIN2A):c.3363T>G(p.Asp1121Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000508 in 1,613,544 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001134407.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151832Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251050Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135654
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461712Hom.: 0 Cov.: 33 AF XY: 0.0000481 AC XY: 35AN XY: 727156
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151832Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74130
ClinVar
Submissions by phenotype
Landau-Kleffner syndrome Uncertain:1Benign:1
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Inborn genetic diseases Uncertain:1
The c.3363T>G (p.D1121E) alteration is located in exon 14 (coding exon 12) of the GRIN2A gene. This alteration results from a T to G substitution at nucleotide position 3363, causing the aspartic acid (D) at amino acid position 1121 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at