chrX-123185881-T-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_007325.5(GRIA3):āc.159T>Cā(p.Phe53Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00101 in 1,205,559 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 390 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_007325.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRIA3 | NM_000828.5 | c.159T>C | p.Phe53Phe | synonymous_variant | 2/16 | ENST00000622768.5 | NP_000819.4 | |
GRIA3 | NM_007325.5 | c.159T>C | p.Phe53Phe | synonymous_variant | 2/16 | ENST00000620443.2 | NP_015564.5 | |
GRIA3 | NM_001256743.2 | c.159T>C | p.Phe53Phe | synonymous_variant | 2/4 | NP_001243672.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRIA3 | ENST00000620443.2 | c.159T>C | p.Phe53Phe | synonymous_variant | 2/16 | 1 | NM_007325.5 | ENSP00000478489.1 | ||
GRIA3 | ENST00000622768.5 | c.159T>C | p.Phe53Phe | synonymous_variant | 2/16 | 5 | NM_000828.5 | ENSP00000481554.1 |
Frequencies
GnomAD3 genomes AF: 0.000843 AC: 94AN: 111487Hom.: 0 Cov.: 22 AF XY: 0.000862 AC XY: 29AN XY: 33655
GnomAD3 exomes AF: 0.000873 AC: 160AN: 183339Hom.: 0 AF XY: 0.000752 AC XY: 51AN XY: 67799
GnomAD4 exome AF: 0.00102 AC: 1118AN: 1094072Hom.: 0 Cov.: 30 AF XY: 0.00100 AC XY: 361AN XY: 359536
GnomAD4 genome AF: 0.000843 AC: 94AN: 111487Hom.: 0 Cov.: 22 AF XY: 0.000862 AC XY: 29AN XY: 33655
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:3
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 29, 2024 | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 15, 2020 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 03, 2015 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 28, 2014 | 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