10-73675239-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001144000.4(AGAP5):c.1421G>A(p.Arg474His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000305 in 1,604,830 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001144000.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGAP5 | NM_001144000.4 | c.1421G>A | p.Arg474His | missense_variant | 8/8 | ENST00000374094.9 | |
BMS1P4-AGAP5 | NR_160426.1 | n.3688G>A | non_coding_transcript_exon_variant | 20/20 | |||
BMS1P4-AGAP5 | NR_160425.1 | n.2900G>A | non_coding_transcript_exon_variant | 19/19 | |||
BMS1P4-AGAP5 | NR_160427.1 | n.2832G>A | non_coding_transcript_exon_variant | 18/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGAP5 | ENST00000374094.9 | c.1421G>A | p.Arg474His | missense_variant | 8/8 | 1 | NM_001144000.4 | A2 | |
SYNPO2L-AS1 | ENST00000668336.1 | n.994C>T | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes AF: 0.0000339 AC: 5AN: 147662Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.0000780 AC: 15AN: 192336Hom.: 2 AF XY: 0.0000385 AC XY: 4AN XY: 103848
GnomAD4 exome AF: 0.0000302 AC: 44AN: 1457056Hom.: 2 Cov.: 37 AF XY: 0.0000235 AC XY: 17AN XY: 724752
GnomAD4 genome AF: 0.0000338 AC: 5AN: 147774Hom.: 0 Cov.: 28 AF XY: 0.0000278 AC XY: 2AN XY: 71940
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at