rs143682696
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP2BP4_StrongBP6_Very_StrongBS2
The NM_205836.3(FBXO38):c.3547G>A(p.Val1183Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000613 in 1,613,944 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 Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V1183L) has been classified as Uncertain significance.
Frequency
Consequence
NM_205836.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBXO38 | NM_205836.3 | c.3547G>A | p.Val1183Ile | missense_variant | 22/22 | ENST00000340253.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBXO38 | ENST00000340253.10 | c.3547G>A | p.Val1183Ile | missense_variant | 22/22 | 5 | NM_205836.3 | P3 | |
FBXO38 | ENST00000394370.7 | c.3322G>A | p.Val1108Ile | missense_variant | 22/22 | 1 | A1 | ||
FBXO38 | ENST00000513826.1 | c.2812G>A | p.Val938Ile | missense_variant | 20/20 | 1 | A1 | ||
FBXO38 | ENST00000296701.10 | c.2812G>A | p.Val938Ile | missense_variant | 21/21 | 2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000834 AC: 127AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000610 AC: 153AN: 250924Hom.: 0 AF XY: 0.000612 AC XY: 83AN XY: 135600
GnomAD4 exome AF: 0.000590 AC: 862AN: 1461636Hom.: 0 Cov.: 31 AF XY: 0.000593 AC XY: 431AN XY: 727130
GnomAD4 genome ? AF: 0.000834 AC: 127AN: 152308Hom.: 0 Cov.: 33 AF XY: 0.000806 AC XY: 60AN XY: 74486
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 22, 2020 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Distal hereditary motor neuropathy type 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 18, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | FBXO38: BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at