12-57475386-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032496.4(ARHGAP9):c.1457A>C(p.Glu486Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000602 in 1,595,744 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032496.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARHGAP9 | NM_032496.4 | c.1457A>C | p.Glu486Ala | missense_variant | 12/18 | ENST00000393791.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARHGAP9 | ENST00000393791.8 | c.1457A>C | p.Glu486Ala | missense_variant | 12/18 | 1 | NM_032496.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000511 AC: 11AN: 215136Hom.: 0 AF XY: 0.0000602 AC XY: 7AN XY: 116338
GnomAD4 exome AF: 0.0000630 AC: 91AN: 1443604Hom.: 0 Cov.: 30 AF XY: 0.0000656 AC XY: 47AN XY: 716454
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2021 | The c.1457A>C (p.E486A) alteration is located in exon 12 (coding exon 11) of the ARHGAP9 gene. This alteration results from a A to C substitution at nucleotide position 1457, causing the glutamic acid (E) at amino acid position 486 to be replaced by an alanine (A). 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