5-148425557-T-C
Variant summary
Our verdict is Benign. Variant got -19 ACMG points: 1P and 20B. PP2BP4_StrongBP6_Very_StrongBA1
The NM_205836.3(FBXO38):āc.1774T>Cā(p.Ser592Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 1,612,442 control chromosomes in the GnomAD database, including 58,593 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S592A) 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 -19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBXO38 | NM_205836.3 | c.1774T>C | p.Ser592Pro | missense_variant | 14/22 | ENST00000340253.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBXO38 | ENST00000340253.10 | c.1774T>C | p.Ser592Pro | missense_variant | 14/22 | 5 | NM_205836.3 | P3 |
Frequencies
GnomAD3 genomes AF: 0.270 AC: 41055AN: 151776Hom.: 5597 Cov.: 32
GnomAD3 exomes AF: 0.268 AC: 67370AN: 251128Hom.: 9182 AF XY: 0.269 AC XY: 36539AN XY: 135710
GnomAD4 exome AF: 0.267 AC: 390551AN: 1460546Hom.: 52985 Cov.: 32 AF XY: 0.268 AC XY: 194653AN XY: 726636
GnomAD4 genome AF: 0.271 AC: 41097AN: 151896Hom.: 5608 Cov.: 32 AF XY: 0.267 AC XY: 19845AN XY: 74252
ClinVar
Submissions by phenotype
Distal hereditary motor neuropathy type 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Neuronopathy, distal hereditary motor, type 2D Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Aug 10, 2021 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 08, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at