rs2253104
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001376558.2(ARFIP2):c.315+61T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 1,588,842 control chromosomes in the GnomAD database, including 227,384 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 0.57 ( 25845 hom., cov: 31)
Exomes 𝑓: 0.52 ( 201539 hom. )
Consequence
ARFIP2
NM_001376558.2 intron
NM_001376558.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0430
Genes affected
ARFIP2 (HGNC:17160): (ADP ribosylation factor interacting protein 2) Enables several functions, including GTP-dependent protein binding activity; membrane curvature sensor activity; and phosphatidylinositol-4-phosphate binding activity. Involved in actin cytoskeleton organization. Located in cell cortex; ruffle; and trans-Golgi network 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=-0.86).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ARFIP2 | NM_001376558.2 | c.315+61T>C | intron_variant | ENST00000396777.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ARFIP2 | ENST00000396777.8 | c.315+61T>C | intron_variant | 2 | NM_001376558.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.569 AC: 86446AN: 151878Hom.: 25817 Cov.: 31
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GnomAD4 exome AF: 0.524 AC: 752488AN: 1436846Hom.: 201539 Cov.: 28 AF XY: 0.522 AC XY: 373087AN XY: 714330
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GnomAD4 genome ? AF: 0.569 AC: 86530AN: 151996Hom.: 25845 Cov.: 31 AF XY: 0.559 AC XY: 41509AN XY: 74288
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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
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at