chr22-42817212-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_014570.5(ARFGAP3):c.994C>T(p.Pro332Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,613,522 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. P332L) 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARFGAP3 | NM_014570.5 | c.994C>T | p.Pro332Ser | missense_variant | 11/16 | ENST00000263245.10 | |
ARFGAP3 | NM_001142293.2 | c.862C>T | p.Pro288Ser | missense_variant | 10/15 | ||
ARFGAP3 | XM_005261525.5 | c.994C>T | p.Pro332Ser | missense_variant | 11/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARFGAP3 | ENST00000263245.10 | c.994C>T | p.Pro332Ser | missense_variant | 11/16 | 1 | NM_014570.5 | P1 | |
ARFGAP3 | ENST00000437119.6 | c.862C>T | p.Pro288Ser | missense_variant | 10/15 | 1 | |||
ARFGAP3 | ENST00000453516.5 | c.535C>T | p.Pro179Ser | missense_variant | 6/8 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251036Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135686
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461374Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 727016
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152148Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74322
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.994C>T (p.P332S) alteration is located in exon 11 (coding exon 11) of the ARFGAP3 gene. This alteration results from a C to T substitution at nucleotide position 994, causing the proline (P) at amino acid position 332 to be replaced by a serine (S). 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