chr17-18246336-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_002018.4(FLII):c.3178C>T(p.Arg1060Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000205 in 1,613,688 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1060H) has been classified as Uncertain significance.
Frequency
Consequence
NM_002018.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLII | NM_002018.4 | c.3178C>T | p.Arg1060Cys | missense_variant | 24/30 | ENST00000327031.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLII | ENST00000327031.9 | c.3178C>T | p.Arg1060Cys | missense_variant | 24/30 | 1 | NM_002018.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251110Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135784
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461472Hom.: 0 Cov.: 34 AF XY: 0.0000206 AC XY: 15AN XY: 727102
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 26, 2022 | The c.3178C>T (p.R1060C) alteration is located in exon 24 (coding exon 24) of the FLII gene. This alteration results from a C to T substitution at nucleotide position 3178, causing the arginine (R) at amino acid position 1060 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at