rs3021274
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_138435.4(FAM83F):c.489+3549T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.563 in 152,112 control chromosomes in the GnomAD database, including 24,996 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 0.56 ( 24993 hom., cov: 33)
Exomes 𝑓: 0.54 ( 3 hom. )
Consequence
FAM83F
NM_138435.4 intron
NM_138435.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.15
Genes affected
FAM83F (HGNC:25148): (family with sequence similarity 83 member F) Predicted to enable protein kinase binding activity. Predicted to be involved in signal transduction. [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=-0.89).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM83F | NM_138435.4 | c.489+3549T>C | intron_variant | ENST00000333407.11 | NP_612444.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FAM83F | ENST00000333407.11 | c.489+3549T>C | intron_variant | 1 | NM_138435.4 | ENSP00000330432.5 | ||||
FAM83F | ENST00000488874.1 | n.516T>C | non_coding_transcript_exon_variant | 3/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.563 AC: 85605AN: 151968Hom.: 24954 Cov.: 33
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GnomAD4 exome AF: 0.542 AC: 13AN: 24Hom.: 3 Cov.: 0 AF XY: 0.417 AC XY: 5AN XY: 12
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GnomAD4 genome AF: 0.563 AC: 85697AN: 152088Hom.: 24993 Cov.: 33 AF XY: 0.556 AC XY: 41343AN XY: 74334
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ClinVar
Not reported inComputational scores
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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