X-123184572-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4BP6_ModerateBS2
The NM_007325.5(GRIA3):c.37C>T(p.Arg13Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000497 in 1,207,778 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 3 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_007325.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRIA3 | NM_000828.5 | c.37C>T | p.Arg13Trp | missense_variant | Exon 1 of 16 | ENST00000622768.5 | NP_000819.4 | |
GRIA3 | NM_007325.5 | c.37C>T | p.Arg13Trp | missense_variant | Exon 1 of 16 | ENST00000620443.2 | NP_015564.5 | |
GRIA3 | NM_001256743.2 | c.37C>T | p.Arg13Trp | 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.37C>T | p.Arg13Trp | missense_variant | Exon 1 of 16 | 1 | NM_007325.5 | ENSP00000478489.1 | ||
GRIA3 | ENST00000622768.5 | c.37C>T | p.Arg13Trp | missense_variant | Exon 1 of 16 | 5 | NM_000828.5 | ENSP00000481554.1 |
Frequencies
GnomAD3 genomes AF: 0.00000903 AC: 1AN: 110729Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32937
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183481Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67911
GnomAD4 exome AF: 0.00000456 AC: 5AN: 1097049Hom.: 0 Cov.: 29 AF XY: 0.00000828 AC XY: 3AN XY: 362421
GnomAD4 genome AF: 0.00000903 AC: 1AN: 110729Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0AN XY: 32937
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
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