19-929824-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005224.3(ARID3A):c.296C>T(p.Pro99Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000192 in 1,545,020 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.296C>T | p.Pro99Leu | missense_variant | 2/9 | ENST00000263620.8 | NP_005215.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARID3A | ENST00000263620.8 | c.296C>T | p.Pro99Leu | missense_variant | 2/9 | 1 | NM_005224.3 | ENSP00000263620.2 |
Frequencies
GnomAD3 genomes AF: 0.000158 AC: 24AN: 152104Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000103 AC: 15AN: 145860Hom.: 0 AF XY: 0.000128 AC XY: 10AN XY: 78250
GnomAD4 exome AF: 0.000195 AC: 272AN: 1392798Hom.: 0 Cov.: 35 AF XY: 0.000191 AC XY: 131AN XY: 687334
GnomAD4 genome AF: 0.000158 AC: 24AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74434
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 02, 2024 | The c.296C>T (p.P99L) alteration is located in exon 2 (coding exon 1) of the ARID3A gene. This alteration results from a C to T substitution at nucleotide position 296, causing the proline (P) at amino acid position 99 to be replaced by a leucine (L). 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