X-123184549-A-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_007325.5(GRIA3):āc.14A>Cā(p.Lys5Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000414 in 1,206,609 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_007325.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRIA3 | NM_000828.5 | c.14A>C | p.Lys5Thr | missense_variant | Exon 1 of 16 | ENST00000622768.5 | NP_000819.4 | |
GRIA3 | NM_007325.5 | c.14A>C | p.Lys5Thr | missense_variant | Exon 1 of 16 | ENST00000620443.2 | NP_015564.5 | |
GRIA3 | NM_001256743.2 | c.14A>C | p.Lys5Thr | missense_variant | Exon 1 of 4 | NP_001243672.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRIA3 | ENST00000620443.2 | c.14A>C | p.Lys5Thr | missense_variant | Exon 1 of 16 | 1 | NM_007325.5 | ENSP00000478489.1 | ||
GRIA3 | ENST00000622768.5 | c.14A>C | p.Lys5Thr | missense_variant | Exon 1 of 16 | 5 | NM_000828.5 | ENSP00000481554.1 |
Frequencies
GnomAD3 genomes AF: 0.00000904 AC: 1AN: 110579Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32807
GnomAD4 exome AF: 0.00000365 AC: 4AN: 1096030Hom.: 0 Cov.: 29 AF XY: 0.00000553 AC XY: 2AN XY: 361464
GnomAD4 genome AF: 0.00000904 AC: 1AN: 110579Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32807
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces lysine, which is basic and polar, with threonine, which is neutral and polar, at codon 5 of the GRIA3 protein (p.Lys5Thr). This variant is present in population databases (no rsID available, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with GRIA3-related conditions. ClinVar contains an entry for this variant (Variation ID: 1429226). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at