chr12-117190416-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015002.3(FBXO21):c.41C>T(p.Pro14Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000996 in 1,475,822 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign 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. P14S) has been classified as Uncertain significance.
Frequency
Consequence
NM_015002.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBXO21 | NM_015002.3 | c.41C>T | p.Pro14Leu | missense_variant | 1/12 | ENST00000622495.5 | |
FBXO21 | NM_033624.3 | c.41C>T | p.Pro14Leu | missense_variant | 1/12 | ||
FBXO21 | XM_017019037.3 | c.41C>T | p.Pro14Leu | missense_variant | 1/11 | ||
FBXO21 | XM_017019038.3 | c.41C>T | p.Pro14Leu | missense_variant | 1/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBXO21 | ENST00000622495.5 | c.41C>T | p.Pro14Leu | missense_variant | 1/12 | 1 | NM_015002.3 | A1 | |
FBXO21 | ENST00000330622.9 | c.41C>T | p.Pro14Leu | missense_variant | 1/12 | 1 | P4 | ||
FBXO21 | ENST00000551458.1 | n.55C>T | non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000401 AC: 61AN: 151982Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000848 AC: 8AN: 94348Hom.: 0 AF XY: 0.0000558 AC XY: 3AN XY: 53720
GnomAD4 exome AF: 0.0000650 AC: 86AN: 1323734Hom.: 0 Cov.: 26 AF XY: 0.0000458 AC XY: 30AN XY: 654610
GnomAD4 genome AF: 0.000401 AC: 61AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 22, 2023 | The c.41C>T (p.P14L) alteration is located in exon 1 (coding exon 1) of the FBXO21 gene. This alteration results from a C to T substitution at nucleotide position 41, causing the proline (P) at amino acid position 14 to be replaced by a leucine (L). 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