chr11-47168177-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032389.6(ARFGAP2):c.1016G>A(p.Arg339His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00126 in 1,614,238 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R339L) has been classified as Likely benign.
Frequency
Consequence
NM_032389.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARFGAP2 | NM_032389.6 | c.1016G>A | p.Arg339His | missense_variant | 11/16 | ENST00000524782.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARFGAP2 | ENST00000524782.6 | c.1016G>A | p.Arg339His | missense_variant | 11/16 | 1 | NM_032389.6 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00619 AC: 943AN: 152228Hom.: 13 Cov.: 31
GnomAD3 exomes AF: 0.00169 AC: 426AN: 251462Hom.: 6 AF XY: 0.00100 AC XY: 136AN XY: 135908
GnomAD4 exome AF: 0.000749 AC: 1095AN: 1461892Hom.: 7 Cov.: 33 AF XY: 0.000609 AC XY: 443AN XY: 727248
GnomAD4 genome ? AF: 0.00620 AC: 944AN: 152346Hom.: 13 Cov.: 31 AF XY: 0.00605 AC XY: 451AN XY: 74496
ClinVar
Submissions by phenotype
ARFGAP2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 12, 2019 | This variant is classified as 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