X-123184535-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_007325.5(GRIA3):c.-1C>T variant causes a 5 prime UTR change. The variant allele was found at a frequency of 0.00000501 in 1,197,202 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 (★).
Frequency
Consequence
NM_007325.5 5_prime_UTR
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.-1C>T | 5_prime_UTR_variant | Exon 1 of 16 | ENST00000622768.5 | NP_000819.4 | ||
GRIA3 | NM_007325.5 | c.-1C>T | 5_prime_UTR_variant | Exon 1 of 16 | ENST00000620443.2 | NP_015564.5 | ||
GRIA3 | NM_001256743.2 | c.-1C>T | 5_prime_UTR_variant | Exon 1 of 4 | NP_001243672.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000904 AC: 1AN: 110612Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32814
GnomAD3 exomes AF: 0.0690 AC: 2AN: 29Hom.: 0 AF XY: 0.105 AC XY: 2AN XY: 19
GnomAD4 exome AF: 0.00000460 AC: 5AN: 1086590Hom.: 0 Cov.: 29 AF XY: 0.00000566 AC XY: 2AN XY: 353162
GnomAD4 genome AF: 0.00000904 AC: 1AN: 110612Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32814
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant occurs in a non-coding region of the GRIA3 gene. It does not change the encoded amino acid sequence of the GRIA3 protein. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with GRIA3-related conditions. Experimental studies and prediction algorithms are not available or were not evaluated, and the effect of this variant on mRNA splicing is currently unknown. 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