rs74402657
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032389.6(ARFGAP2):c.619+226G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00294 in 588,404 control chromosomes in the GnomAD database, including 44 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0023 ( 14 hom., cov: 33)
Exomes 𝑓: 0.0032 ( 30 hom. )
Consequence
ARFGAP2
NM_032389.6 intron
NM_032389.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.423
Genes affected
ARFGAP2 (HGNC:13504): (ADP ribosylation factor GTPase activating protein 2) Predicted to enable GTPase activator activity. Predicted to be involved in COPI coating of Golgi vesicle. Located in Golgi apparatus; cytosol; and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.65).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0502 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARFGAP2 | NM_032389.6 | c.619+226G>C | intron_variant | ENST00000524782.6 | NP_115765.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARFGAP2 | ENST00000524782.6 | c.619+226G>C | intron_variant | 1 | NM_032389.6 | ENSP00000434442.1 |
Frequencies
GnomAD3 genomes AF: 0.00229 AC: 349AN: 152210Hom.: 14 Cov.: 33
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GnomAD4 exome AF: 0.00318 AC: 1385AN: 436076Hom.: 30 Cov.: 5 AF XY: 0.00286 AC XY: 658AN XY: 229940
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GnomAD4 genome AF: 0.00227 AC: 346AN: 152328Hom.: 14 Cov.: 33 AF XY: 0.00252 AC XY: 188AN XY: 74482
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at