19-932458-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005224.3(ARID3A):c.409G>A(p.Gly137Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000125 in 1,587,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005224.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARID3A | NM_005224.3 | c.409G>A | p.Gly137Arg | missense_variant | 3/9 | ENST00000263620.8 | NP_005215.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARID3A | ENST00000263620.8 | c.409G>A | p.Gly137Arg | missense_variant | 3/9 | 1 | NM_005224.3 | ENSP00000263620 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000177 AC: 27AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000126 AC: 27AN: 213540Hom.: 0 AF XY: 0.000101 AC XY: 12AN XY: 118738
GnomAD4 exome AF: 0.000120 AC: 172AN: 1435608Hom.: 0 Cov.: 34 AF XY: 0.000116 AC XY: 83AN XY: 714776
GnomAD4 genome AF: 0.000177 AC: 27AN: 152284Hom.: 0 Cov.: 33 AF XY: 0.000201 AC XY: 15AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2022 | The c.409G>A (p.G137R) alteration is located in exon 3 (coding exon 2) of the ARID3A gene. This alteration results from a G to A substitution at nucleotide position 409, causing the glycine (G) at amino acid position 137 to be replaced by an arginine (R). 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