chr22-42808877-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_014570.5(ARFGAP3):āc.1210C>Gā(p.Arg404Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00000621 in 1,609,890 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R404C) 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.1210C>G | p.Arg404Gly | missense_variant | 13/16 | ENST00000263245.10 | |
ARFGAP3 | NM_001142293.2 | c.1078C>G | p.Arg360Gly | missense_variant | 12/15 | ||
ARFGAP3 | XM_005261525.5 | c.1078C>G | p.Arg360Gly | missense_variant | 12/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARFGAP3 | ENST00000263245.10 | c.1210C>G | p.Arg404Gly | missense_variant | 13/16 | 1 | NM_014570.5 | P1 | |
ARFGAP3 | ENST00000437119.6 | c.1078C>G | p.Arg360Gly | missense_variant | 12/15 | 1 | |||
ARFGAP3 | ENST00000453516.5 | c.619C>G | p.Arg207Gly | missense_variant | 7/8 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152144Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249450Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134846
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1457746Hom.: 0 Cov.: 30 AF XY: 0.00000414 AC XY: 3AN XY: 725042
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152144Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 15, 2023 | The c.1210C>G (p.R404G) alteration is located in exon 13 (coding exon 13) of the ARFGAP3 gene. This alteration results from a C to G substitution at nucleotide position 1210, causing the arginine (R) at amino acid position 404 to be replaced by a glycine (G). 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