chr11-47166876-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032389.6(ARFGAP2):c.1216C>T(p.Arg406Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0014 in 1,613,546 control chromosomes in the GnomAD database, including 21 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. R406Q) has been classified as Uncertain significance.
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.1216C>T | p.Arg406Trp | missense_variant | 13/16 | ENST00000524782.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARFGAP2 | ENST00000524782.6 | c.1216C>T | p.Arg406Trp | missense_variant | 13/16 | 1 | NM_032389.6 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00551 AC: 839AN: 152164Hom.: 12 Cov.: 33
GnomAD3 exomes AF: 0.00227 AC: 568AN: 250754Hom.: 8 AF XY: 0.00182 AC XY: 247AN XY: 135592
GnomAD4 exome AF: 0.000977 AC: 1428AN: 1461264Hom.: 9 Cov.: 34 AF XY: 0.000860 AC XY: 625AN XY: 726964
GnomAD4 genome ? AF: 0.00550 AC: 838AN: 152282Hom.: 12 Cov.: 33 AF XY: 0.00529 AC XY: 394AN XY: 74456
ClinVar
Submissions by phenotype
ARFGAP2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 04, 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