rs2071242
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002018.4(FLII):c.1596+69A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 1,535,390 control chromosomes in the GnomAD database, including 42,476 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 0.22 ( 3883 hom., cov: 33)
Exomes 𝑓: 0.23 ( 38593 hom. )
Consequence
FLII
NM_002018.4 intron
NM_002018.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.17
Genes affected
FLII (HGNC:3750): (FLII actin remodeling protein) This gene encodes a protein with a gelsolin-like actin binding domain and an N-terminal leucine-rich repeat-protein protein interaction domain. The protein is similar to a Drosophila protein involved in early embryogenesis and the structural organization of indirect flight muscle. The gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Jul 2008]
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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 (EAS) allele frequency at 95% confidence interval = 0.296 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLII | NM_002018.4 | c.1596+69A>G | intron_variant | ENST00000327031.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLII | ENST00000327031.9 | c.1596+69A>G | intron_variant | 1 | NM_002018.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.220 AC: 33450AN: 151994Hom.: 3876 Cov.: 33
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GnomAD4 exome AF: 0.234 AC: 324379AN: 1383278Hom.: 38593 Cov.: 24 AF XY: 0.234 AC XY: 160074AN XY: 685162
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GnomAD4 genome ? AF: 0.220 AC: 33476AN: 152112Hom.: 3883 Cov.: 33 AF XY: 0.219 AC XY: 16295AN XY: 74354
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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