chr12-57731880-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001122772.3(AGAP2):c.1882G>A(p.Ala628Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000683 in 1,610,398 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001122772.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGAP2 | NM_001122772.3 | c.1882G>A | p.Ala628Thr | missense_variant | 8/19 | ENST00000547588.6 | |
AGAP2 | NM_014770.4 | c.874G>A | p.Ala292Thr | missense_variant | 8/18 | ||
AGAP2 | XM_005268625.4 | c.1882G>A | p.Ala628Thr | missense_variant | 8/18 | ||
AGAP2 | XM_005268626.3 | c.874G>A | p.Ala292Thr | missense_variant | 8/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGAP2 | ENST00000547588.6 | c.1882G>A | p.Ala628Thr | missense_variant | 8/19 | 1 | NM_001122772.3 | P3 | |
AGAP2 | ENST00000257897.7 | c.874G>A | p.Ala292Thr | missense_variant | 8/18 | 1 | A1 | ||
AGAP2 | ENST00000328568.9 | c.1474G>A | p.Ala492Thr | missense_variant | 8/18 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000822 AC: 2AN: 243378Hom.: 0 AF XY: 0.00000761 AC XY: 1AN XY: 131392
GnomAD4 exome AF: 0.00000686 AC: 10AN: 1458218Hom.: 0 Cov.: 33 AF XY: 0.00000414 AC XY: 3AN XY: 725172
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2022 | The c.1882G>A (p.A628T) alteration is located in exon 8 (coding exon 8) of the AGAP2 gene. This alteration results from a G to A substitution at nucleotide position 1882, causing the alanine (A) at amino acid position 628 to be replaced by a threonine (T). 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