19-932638-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005224.3(ARID3A):c.589C>T(p.Arg197Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000182 in 1,536,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R197Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_005224.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARID3A | NM_005224.3 | c.589C>T | p.Arg197Trp | missense_variant | 3/9 | ENST00000263620.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARID3A | ENST00000263620.8 | c.589C>T | p.Arg197Trp | missense_variant | 3/9 | 1 | NM_005224.3 | P1 | |
ARID3A | ENST00000587532.5 | c.130C>T | p.Arg44Trp | missense_variant | 1/6 | 5 | |||
ARID3A | ENST00000457152.3 | c.76C>T | p.Arg26Trp | missense_variant, NMD_transcript_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152236Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000173 AC: 24AN: 1383926Hom.: 0 Cov.: 37 AF XY: 0.0000161 AC XY: 11AN XY: 682414
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152236Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74384
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 2021 | The c.589C>T (p.R197W) alteration is located in exon 3 (coding exon 2) of the ARID3A gene. This alteration results from a C to T substitution at nucleotide position 589, causing the arginine (R) at amino acid position 197 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at