chr10-73675135-G-C
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001144000.4(AGAP5):āc.1525C>Gā(p.Leu509Val) variant causes a missense change. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.00040 ( 0 hom., cov: 28)
Exomes š: 0.00082 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
AGAP5
NM_001144000.4 missense
NM_001144000.4 missense
Scores
1
3
10
Clinical Significance
Conservation
PhyloP100: 5.20
Genes affected
AGAP5 (HGNC:23467): (ArfGAP with GTPase domain, ankyrin repeat and PH domain 5) Predicted to enable GTPase activator activity and metal ion binding activity. Predicted to be involved in regulation of catalytic activity. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
SYNPO2L-AS1 (HGNC:55242): (SYNPO2L antisense RNA 1)
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGAP5 | NM_001144000.4 | c.1525C>G | p.Leu509Val | missense_variant | 8/8 | ENST00000374094.9 | |
BMS1P4-AGAP5 | NR_160426.1 | n.3792C>G | non_coding_transcript_exon_variant | 20/20 | |||
BMS1P4-AGAP5 | NR_160425.1 | n.3004C>G | non_coding_transcript_exon_variant | 19/19 | |||
BMS1P4-AGAP5 | NR_160427.1 | n.2936C>G | non_coding_transcript_exon_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGAP5 | ENST00000374094.9 | c.1525C>G | p.Leu509Val | missense_variant | 8/8 | 1 | NM_001144000.4 | A2 | |
SYNPO2L-AS1 | ENST00000668336.1 | n.890G>C | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 60AN: 149640Hom.: 0 Cov.: 28 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000819 AC: 1196AN: 1460642Hom.: 0 Cov.: 37 AF XY: 0.000812 AC XY: 590AN XY: 726576
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000401 AC: 60AN: 149758Hom.: 0 Cov.: 28 AF XY: 0.000369 AC XY: 27AN XY: 73084
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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 | Apr 24, 2024 | The c.1525C>G (p.L509V) alteration is located in exon 8 (coding exon 8) of the AGAP5 gene. This alteration results from a C to G substitution at nucleotide position 1525, causing the leucine (L) at amino acid position 509 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Pathogenic
D;D;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D
MetaSVM
Benign
T
MutationTaster
Benign
D;D
PrimateAI
Benign
T
Sift4G
Uncertain
D;D;D
Polyphen
0.58
.;.;P
Vest4
MutPred
Gain of MoRF binding (P = 0.0904);.;Gain of MoRF binding (P = 0.0904);
MVP
ClinPred
T
Varity_R
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