19-929637-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_005224.3(ARID3A):c.109G>A(p.Gly37Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000334 in 1,528,940 control chromosomes in the GnomAD database, including 6 homozygotes. 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 151970Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000951 AC: 12AN: 126172Hom.: 0 AF XY: 0.0000720 AC XY: 5AN XY: 69456
GnomAD4 exome AF: 0.000352 AC: 484AN: 1376860Hom.: 6 Cov.: 70 AF XY: 0.000331 AC XY: 225AN XY: 679424
GnomAD4 genome AF: 0.000171 AC: 26AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.109G>A (p.G37S) alteration is located in exon 2 (coding exon 1) of the ARID3A gene. This alteration results from a G to A substitution at nucleotide position 109, causing the glycine (G) at amino acid position 37 to be replaced by a serine (S). 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