chr12-57730531-T-G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_001122772.3(AGAP2):ā€‹c.2392A>Cā€‹(p.Lys798Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000256 in 1,614,086 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.000053 ( 0 hom., cov: 33)
Exomes š‘“: 0.00028 ( 0 hom. )

Consequence

AGAP2
NM_001122772.3 missense

Scores

3
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 2.25
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.16248244).
BS2
High AC in GnomAd4 at 8 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
AGAP2NM_001122772.3 linkuse as main transcriptc.2392A>C p.Lys798Gln missense_variant 12/19 ENST00000547588.6 NP_001116244.1
AGAP2NM_014770.4 linkuse as main transcriptc.1384A>C p.Lys462Gln missense_variant 12/18 NP_055585.1
AGAP2XM_005268625.4 linkuse as main transcriptc.2392A>C p.Lys798Gln missense_variant 12/18 XP_005268682.1
AGAP2XM_005268626.3 linkuse as main transcriptc.1384A>C p.Lys462Gln missense_variant 12/19 XP_005268683.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
AGAP2ENST00000547588.6 linkuse as main transcriptc.2392A>C p.Lys798Gln missense_variant 12/191 NM_001122772.3 ENSP00000449241 P3
AGAP2ENST00000257897.7 linkuse as main transcriptc.1384A>C p.Lys462Gln missense_variant 12/181 ENSP00000257897 A1Q99490-2
AGAP2ENST00000328568.9 linkuse as main transcriptc.1984A>C p.Lys662Gln missense_variant 12/185 ENSP00000328160
AGAP2ENST00000549129.1 linkuse as main transcriptc.460A>C p.Lys154Gln missense_variant 5/53 ENSP00000446683

Frequencies

GnomAD3 genomes
AF:
0.0000526
AC:
8
AN:
152214
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000118
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000835
AC:
21
AN:
251428
Hom.:
0
AF XY:
0.000110
AC XY:
15
AN XY:
135888
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000185
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000278
AC:
406
AN:
1461872
Hom.:
0
Cov.:
30
AF XY:
0.000265
AC XY:
193
AN XY:
727232
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.000359
Gnomad4 OTH exome
AF:
0.000116
GnomAD4 genome
AF:
0.0000526
AC:
8
AN:
152214
Hom.:
0
Cov.:
33
AF XY:
0.0000403
AC XY:
3
AN XY:
74370
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000118
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000114
Hom.:
0
Bravo
AF:
0.0000491
ExAC
AF:
0.0000494
AC:
6
EpiCase
AF:
0.0000545
EpiControl
AF:
0.000237

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 submitterclinical testingAmbry GeneticsFeb 27, 2023The c.2392A>C (p.K798Q) alteration is located in exon 12 (coding exon 12) of the AGAP2 gene. This alteration results from a A to C substitution at nucleotide position 2392, causing the lysine (K) at amino acid position 798 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.29
CADD
Uncertain
23
DANN
Uncertain
0.97
DEOGEN2
Benign
0.033
.;.;T
Eigen
Benign
-0.018
Eigen_PC
Benign
0.12
FATHMM_MKL
Uncertain
0.91
D
LIST_S2
Benign
0.85
D;D;D
M_CAP
Benign
0.0093
T
MetaRNN
Benign
0.16
T;T;T
MetaSVM
Benign
-1.0
T
MutationTaster
Benign
0.63
D;N
PrimateAI
Uncertain
0.77
T
PROVEAN
Benign
-0.64
N;N;N
REVEL
Benign
0.13
Sift
Benign
0.24
T;D;D
Sift4G
Benign
0.18
T;T;D
Polyphen
0.86
P;B;.
Vest4
0.47
MVP
0.49
MPC
1.3
ClinPred
0.13
T
GERP RS
4.5
gMVP
0.19

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs752956684; hg19: chr12-58124314; API