rs1055447
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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.*609G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,114 control chromosomes in the GnomAD database, including 20,513 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 0.52 ( 20486 hom., cov: 31)
Exomes 𝑓: 0.47 ( 27 hom. )
Consequence
ARFGAP2
NM_032389.6 3_prime_UTR
NM_032389.6 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.17
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=-0.59).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.624 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARFGAP2 | NM_032389.6 | c.*609G>T | 3_prime_UTR_variant | 16/16 | ENST00000524782.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARFGAP2 | ENST00000524782.6 | c.*609G>T | 3_prime_UTR_variant | 16/16 | 1 | NM_032389.6 | A1 | ||
ARFGAP2 | ENST00000426335.6 | c.*609G>T | 3_prime_UTR_variant | 15/15 | 2 | ||||
ARFGAP2 | ENST00000525314.6 | c.*609G>T | 3_prime_UTR_variant | 17/17 | 3 | P3 | |||
ARFGAP2 | ENST00000627920.2 | c.*609G>T | 3_prime_UTR_variant | 11/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.515 AC: 78218AN: 151794Hom.: 20475 Cov.: 31
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GnomAD4 exome AF: 0.465 AC: 94AN: 202Hom.: 27 Cov.: 0 AF XY: 0.426 AC XY: 52AN XY: 122
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GnomAD4 genome ? AF: 0.515 AC: 78259AN: 151912Hom.: 20486 Cov.: 31 AF XY: 0.513 AC XY: 38111AN XY: 74258
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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