chr19-929752-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.224C>T(p.Pro75Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000515 in 1,554,800 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
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152104Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.0000952 AC: 15AN: 157588Hom.: 0 AF XY: 0.0000807 AC XY: 7AN XY: 86768
GnomAD4 exome AF: 0.0000499 AC: 70AN: 1402696Hom.: 0 Cov.: 75 AF XY: 0.0000432 AC XY: 30AN XY: 693928
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152104Hom.: 0 Cov.: 34 AF XY: 0.0000808 AC XY: 6AN XY: 74294
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.224C>T (p.P75L) 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 224, causing the proline (P) at amino acid position 75 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