chr5-148427440-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 1P and 9B. PP2BP4_StrongBP6BS2
The NM_205836.3(FBXO38):āc.2146A>Gā(p.Ser716Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000565 in 1,614,202 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_205836.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FBXO38 | NM_205836.3 | c.2146A>G | p.Ser716Gly | missense_variant | 15/22 | ENST00000340253.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FBXO38 | ENST00000340253.10 | c.2146A>G | p.Ser716Gly | missense_variant | 15/22 | 5 | NM_205836.3 | P3 | |
FBXO38 | ENST00000394370.7 | c.2146A>G | p.Ser716Gly | missense_variant | 15/22 | 1 | A1 | ||
FBXO38 | ENST00000513826.1 | c.1918+1739A>G | intron_variant | 1 | A1 | ||||
FBXO38 | ENST00000296701.10 | c.1918+1739A>G | intron_variant | 2 | A1 |
Frequencies
GnomAD3 genomes AF: 0.000519 AC: 79AN: 152212Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000718 AC: 180AN: 250750Hom.: 1 AF XY: 0.000871 AC XY: 118AN XY: 135540
GnomAD4 exome AF: 0.000570 AC: 833AN: 1461872Hom.: 3 Cov.: 32 AF XY: 0.000591 AC XY: 430AN XY: 727236
GnomAD4 genome AF: 0.000519 AC: 79AN: 152330Hom.: 1 Cov.: 32 AF XY: 0.000510 AC XY: 38AN XY: 74494
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 30, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2017 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 29, 2019 | 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 21, 2024 | - - |
FBXO38-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 04, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at