1-16250846-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_018994.3(FBXO42):c.1978G>A(p.Val660Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000632 in 1,614,038 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 (★).
Frequency
Consequence
NM_018994.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FBXO42 | NM_018994.3 | c.1978G>A | p.Val660Ile | missense_variant | Exon 10 of 10 | ENST00000375592.8 | NP_061867.1 | |
FBXO42 | XM_047422747.1 | c.1978G>A | p.Val660Ile | missense_variant | Exon 12 of 12 | XP_047278703.1 | ||
FBXO42 | XM_047422750.1 | c.1978G>A | p.Val660Ile | missense_variant | Exon 12 of 12 | XP_047278706.1 | ||
FBXO42 | XM_047422751.1 | c.1978G>A | p.Val660Ile | missense_variant | Exon 12 of 12 | XP_047278707.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FBXO42 | ENST00000375592.8 | c.1978G>A | p.Val660Ile | missense_variant | Exon 10 of 10 | 1 | NM_018994.3 | ENSP00000364742.3 | ||
FBXO42 | ENST00000444116.1 | c.*236G>A | downstream_gene_variant | 5 | ENSP00000412416.1 | |||||
FBXO42 | ENST00000456164.5 | c.*236G>A | downstream_gene_variant | 2 | ENSP00000415663.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251490Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135918
GnomAD4 exome AF: 0.0000677 AC: 99AN: 1461894Hom.: 0 Cov.: 30 AF XY: 0.0000756 AC XY: 55AN XY: 727248
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1978G>A (p.V660I) alteration is located in exon 10 (coding exon 9) of the FBXO42 gene. This alteration results from a G to A substitution at nucleotide position 1978, causing the valine (V) at amino acid position 660 to be replaced by an isoleucine (I). 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