chr12-57730883-C-T
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Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001122772.3(AGAP2):c.2216G>A(p.Arg739Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000497 in 1,609,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
AGAP2
NM_001122772.3 missense
NM_001122772.3 missense
Scores
7
7
3
Clinical Significance
Conservation
PhyloP100: 7.69
Genes affected
AGAP2 (HGNC:16921): (ArfGAP with GTPase domain, ankyrin repeat and PH domain 2) The protein encoded by this gene belongs to the centaurin gamma-like family. It mediates anti-apoptotic effects of nerve growth factor by activating nuclear phosphoinositide 3-kinase. It is overexpressed in cancer cells, and promotes cancer cell invasion. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.763
BS2
High AC in GnomAdExome4 at 6 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGAP2 | NM_001122772.3 | c.2216G>A | p.Arg739Gln | missense_variant | 11/19 | ENST00000547588.6 | NP_001116244.1 | |
AGAP2 | NM_014770.4 | c.1208G>A | p.Arg403Gln | missense_variant | 11/18 | NP_055585.1 | ||
AGAP2 | XM_005268625.4 | c.2216G>A | p.Arg739Gln | missense_variant | 11/18 | XP_005268682.1 | ||
AGAP2 | XM_005268626.3 | c.1208G>A | p.Arg403Gln | missense_variant | 11/19 | XP_005268683.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGAP2 | ENST00000547588.6 | c.2216G>A | p.Arg739Gln | missense_variant | 11/19 | 1 | NM_001122772.3 | ENSP00000449241 | P3 | |
AGAP2 | ENST00000257897.7 | c.1208G>A | p.Arg403Gln | missense_variant | 11/18 | 1 | ENSP00000257897 | A1 | ||
AGAP2 | ENST00000328568.9 | c.1808G>A | p.Arg603Gln | missense_variant | 11/18 | 5 | ENSP00000328160 | |||
AGAP2 | ENST00000549129.1 | c.284G>A | p.Arg95Gln | missense_variant | 4/5 | 3 | ENSP00000446683 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000415 AC: 1AN: 241146Hom.: 0 AF XY: 0.00000766 AC XY: 1AN XY: 130522
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GnomAD4 exome AF: 0.00000412 AC: 6AN: 1457020Hom.: 0 Cov.: 34 AF XY: 0.00000276 AC XY: 2AN XY: 724502
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74370
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2022 | The c.2216G>A (p.R739Q) alteration is located in exon 11 (coding exon 11) of the AGAP2 gene. This alteration results from a G to A substitution at nucleotide position 2216, causing the arginine (R) at amino acid position 739 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Uncertain
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
.;.;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
T
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Uncertain
D;D;D
REVEL
Pathogenic
Sift
Uncertain
D;D;T
Sift4G
Benign
T;T;D
Polyphen
D;D;.
Vest4
MutPred
0.43
.;Loss of methylation at R739 (P = 0.0284);.;
MVP
MPC
1.5
ClinPred
D
GERP RS
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at