10-47503383-C-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001190810.1(AGAP9):c.746G>T(p.Arg249Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001190810.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGAP9 | NM_001190810.1 | c.746G>T | p.Arg249Leu | missense_variant | Exon 8 of 8 | ENST00000452145.6 | NP_001177739.1 | |
ANXA8 | XM_006717951.4 | c.94-23495G>T | intron_variant | Intron 1 of 11 | XP_006718014.1 | |||
BMS1P2-AGAP9 | NR_160414.1 | n.1804G>T | non_coding_transcript_exon_variant | Exon 16 of 16 | ||||
BMS1P2-AGAP9 | NR_160415.1 | n.2161G>T | non_coding_transcript_exon_variant | Exon 16 of 16 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 115AN: 148434Hom.: 10 Cov.: 26 FAILED QC
GnomAD3 exomes AF: 0.0000136 AC: 1AN: 73398Hom.: 0 AF XY: 0.0000277 AC XY: 1AN XY: 36166
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000125 AC: 182AN: 1461280Hom.: 13 Cov.: 33 AF XY: 0.0000990 AC XY: 72AN XY: 726944
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000788 AC: 117AN: 148542Hom.: 11 Cov.: 26 AF XY: 0.000745 AC XY: 54AN XY: 72520
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.746G>T (p.R249L) alteration is located in exon 8 (coding exon 8) of the AGAP9 gene. This alteration results from a G to T substitution at nucleotide position 746, causing the arginine (R) at amino acid position 249 to be replaced by a leucine (L). 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