chrX-47624384-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001145252.3(CFP):c.1301G>A(p.Arg434Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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. R434T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001145252.3 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 |
---|---|---|---|---|---|---|---|
CFP | NM_001145252.3 | c.1301G>A | p.Arg434Lys | missense_variant | 9/9 | ENST00000396992.8 | |
CFP | NM_002621.2 | c.1301G>A | p.Arg434Lys | missense_variant | 10/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CFP | ENST00000396992.8 | c.1301G>A | p.Arg434Lys | missense_variant | 9/9 | 1 | NM_001145252.3 | P1 | |
CFP | ENST00000247153.7 | c.1301G>A | p.Arg434Lys | missense_variant | 10/10 | 5 | P1 | ||
CFP | ENST00000478222.1 | n.422G>A | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
CFP | ENST00000640573.1 | n.1539G>A | non_coding_transcript_exon_variant | 7/7 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 21
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 21
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 07, 2022 | This sequence change replaces arginine, which is basic and polar, with lysine, which is basic and polar, at codon 434 of the CFP protein (p.Arg434Lys). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CFP protein function. This variant has not been reported in the literature in individuals affected with CFP-related conditions. This variant is not present in population databases (gnomAD no frequency). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.