NM_000828.5:c.1181G>A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_000828.5(GRIA3):c.1181G>A(p.Arg394Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00102 in 1,036,915 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 369 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_000828.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRIA3 | NM_000828.5 | c.1181G>A | p.Arg394Gln | missense_variant | Exon 8 of 16 | ENST00000622768.5 | NP_000819.4 | |
GRIA3 | NM_007325.5 | c.1181G>A | p.Arg394Gln | missense_variant | Exon 8 of 16 | ENST00000620443.2 | NP_015564.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRIA3 | ENST00000620443.2 | c.1181G>A | p.Arg394Gln | missense_variant | Exon 8 of 16 | 1 | NM_007325.5 | ENSP00000478489.1 | ||
GRIA3 | ENST00000622768.5 | c.1181G>A | p.Arg394Gln | missense_variant | Exon 8 of 16 | 5 | NM_000828.5 | ENSP00000481554.1 | ||
GRIA3 | ENST00000620581.4 | n.1181G>A | non_coding_transcript_exon_variant | Exon 8 of 17 | 1 | ENSP00000481875.1 |
Frequencies
GnomAD3 genomes AF: 0.000901 AC: 101AN: 112111Hom.: 0 Cov.: 22 AF XY: 0.000757 AC XY: 26AN XY: 34343
GnomAD3 exomes AF: 0.00148 AC: 271AN: 183088Hom.: 1 AF XY: 0.00170 AC XY: 115AN XY: 67650
GnomAD4 exome AF: 0.00104 AC: 959AN: 924747Hom.: 0 Cov.: 17 AF XY: 0.00137 AC XY: 343AN XY: 251247
GnomAD4 genome AF: 0.000900 AC: 101AN: 112168Hom.: 0 Cov.: 22 AF XY: 0.000756 AC XY: 26AN XY: 34410
ClinVar
Submissions by phenotype
not specified Benign:5
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not provided Benign:3
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Syndromic X-linked intellectual disability 94 Benign:1
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Inborn genetic diseases Benign:1
This alteration is classified as 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. -
GRIA3-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at