chr20-48952867-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PM2PP2PP3_ModerateBS1_Supporting
The NM_006420.3(ARFGEF2):c.586C>T(p.Arg196Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000347 in 1,614,096 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R196H) has been classified as Uncertain significance.
Frequency
Consequence
NM_006420.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARFGEF2 | NM_006420.3 | c.586C>T | p.Arg196Cys | missense_variant | 5/39 | ENST00000371917.5 | |
ARFGEF2 | NM_001410846.1 | c.586C>T | p.Arg196Cys | missense_variant | 5/39 | ||
ARFGEF2 | XM_047439832.1 | c.22C>T | p.Arg8Cys | missense_variant | 3/37 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARFGEF2 | ENST00000371917.5 | c.586C>T | p.Arg196Cys | missense_variant | 5/39 | 1 | NM_006420.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152218Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.0000358 AC XY: 26AN XY: 727244
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 22, 2016 | - - |
Periventricular heterotopia with microcephaly, autosomal recessive Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | Apr 04, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at