22-38961534-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_145699.4(APOBEC3A):c.322G>A(p.Gly108Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000151 in 1,395,194 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_145699.4 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 |
---|---|---|---|---|---|---|---|---|
APOBEC3A | NM_145699.4 | c.322G>A | p.Gly108Arg | missense_variant | 3/5 | ENST00000249116.7 | NP_663745.1 | |
APOBEC3A | NM_001270406.2 | c.268G>A | p.Gly90Arg | missense_variant | 3/5 | NP_001257335.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APOBEC3A | ENST00000249116.7 | c.322G>A | p.Gly108Arg | missense_variant | 3/5 | 1 | NM_145699.4 | ENSP00000249116 | P1 | |
APOBEC3A | ENST00000402255.5 | c.322G>A | p.Gly108Arg | missense_variant | 4/6 | 5 | ENSP00000384359 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 134320Hom.: 0 Cov.: 18 FAILED QC
GnomAD3 exomes AF: 0.0000209 AC: 5AN: 239094Hom.: 0 AF XY: 0.0000233 AC XY: 3AN XY: 128994
GnomAD4 exome AF: 0.0000151 AC: 21AN: 1395194Hom.: 1 Cov.: 31 AF XY: 0.0000101 AC XY: 7AN XY: 694662
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 134320Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0AN XY: 64884
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2024 | The c.322G>A (p.G108R) alteration is located in exon 3 (coding exon 3) of the APOBEC3A gene. This alteration results from a G to A substitution at nucleotide position 322, causing the glycine (G) at amino acid position 108 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