11-47168177-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_032389.6(ARFGAP2):c.1016G>T(p.Arg339Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000183 in 1,614,236 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R339H) 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.1016G>T | p.Arg339Leu | missense_variant | 11/16 | ENST00000524782.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARFGAP2 | ENST00000524782.6 | c.1016G>T | p.Arg339Leu | missense_variant | 11/16 | 1 | NM_032389.6 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000263 AC: 40AN: 152226Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000513 AC: 129AN: 251462Hom.: 0 AF XY: 0.000515 AC XY: 70AN XY: 135908
GnomAD4 exome AF: 0.000174 AC: 255AN: 1461892Hom.: 1 Cov.: 33 AF XY: 0.000186 AC XY: 135AN XY: 727248
GnomAD4 genome ? AF: 0.000263 AC: 40AN: 152344Hom.: 0 Cov.: 31 AF XY: 0.000295 AC XY: 22AN XY: 74494
ClinVar
Submissions by phenotype
ARFGAP2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 18, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at