chr22-42808879-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014570.5(ARFGAP3):c.1208G>A(p.Arg403His) variant causes a missense change. The variant allele was found at a frequency of 0.0000199 in 1,608,684 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. R403P) has been classified as Uncertain significance.
Frequency
Consequence
NM_014570.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARFGAP3 | NM_014570.5 | c.1208G>A | p.Arg403His | missense_variant | 13/16 | ENST00000263245.10 | |
ARFGAP3 | NM_001142293.2 | c.1076G>A | p.Arg359His | missense_variant | 12/15 | ||
ARFGAP3 | XM_005261525.5 | c.1076G>A | p.Arg359His | missense_variant | 12/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARFGAP3 | ENST00000263245.10 | c.1208G>A | p.Arg403His | missense_variant | 13/16 | 1 | NM_014570.5 | P1 | |
ARFGAP3 | ENST00000437119.6 | c.1076G>A | p.Arg359His | missense_variant | 12/15 | 1 | |||
ARFGAP3 | ENST00000453516.5 | c.617G>A | p.Arg206His | missense_variant | 7/8 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152106Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000402 AC: 10AN: 248780Hom.: 0 AF XY: 0.0000372 AC XY: 5AN XY: 134498
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1456578Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 724370
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152106Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74306
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at