11-47166875-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032389.6(ARFGAP2):c.1217G>A(p.Arg406Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000676 in 1,613,538 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R406W) has been classified as Benign.
Frequency
Consequence
NM_032389.6 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 |
---|---|---|---|---|---|---|---|
ARFGAP2 | NM_032389.6 | c.1217G>A | p.Arg406Gln | missense_variant | 13/16 | ENST00000524782.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARFGAP2 | ENST00000524782.6 | c.1217G>A | p.Arg406Gln | missense_variant | 13/16 | 1 | NM_032389.6 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250802Hom.: 0 AF XY: 0.000111 AC XY: 15AN XY: 135618
GnomAD4 exome AF: 0.0000684 AC: 100AN: 1461320Hom.: 0 Cov.: 33 AF XY: 0.0000729 AC XY: 53AN XY: 726988
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 04, 2023 | The c.1217G>A (p.R406Q) alteration is located in exon 13 (coding exon 13) of the ARFGAP2 gene. This alteration results from a G to A substitution at nucleotide position 1217, causing the arginine (R) at amino acid position 406 to be replaced by a glutamine (Q). 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