chrX-153700974-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001256447.2(BCAP31):c.704C>T(p.Ala235Val) variant causes a missense, splice region 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. 16/21 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. 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. A235T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001256447.2 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
BCAP31 | NM_001256447.2 | c.704C>T | p.Ala235Val | missense_variant, splice_region_variant | 8/8 | ENST00000345046.12 | |
BCAP31 | NM_001139457.2 | c.905C>T | p.Ala302Val | missense_variant, splice_region_variant | 8/8 | ||
BCAP31 | NM_001139441.1 | c.704C>T | p.Ala235Val | missense_variant, splice_region_variant | 8/8 | ||
BCAP31 | NM_005745.8 | c.704C>T | p.Ala235Val | missense_variant, splice_region_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAP31 | ENST00000345046.12 | c.704C>T | p.Ala235Val | missense_variant, splice_region_variant | 8/8 | 1 | NM_001256447.2 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 23
GnomAD4 exome Cov.: 29
GnomAD4 genome ? Cov.: 23
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Aug 04, 2023 | This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 235 of the BCAP31 protein (p.Ala235Val). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with BCAP31-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The valine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.