chrX-153700962-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001256447.2(BCAP31):c.716G>A(p.Gly239Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000913 in 1,205,017 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001256447.2 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 |
---|---|---|---|---|---|---|---|
BCAP31 | NM_001256447.2 | c.716G>A | p.Gly239Asp | missense_variant | 8/8 | ENST00000345046.12 | |
BCAP31 | NM_001139457.2 | c.917G>A | p.Gly306Asp | missense_variant | 8/8 | ||
BCAP31 | NM_001139441.1 | c.716G>A | p.Gly239Asp | missense_variant | 8/8 | ||
BCAP31 | NM_005745.8 | c.716G>A | p.Gly239Asp | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAP31 | ENST00000345046.12 | c.716G>A | p.Gly239Asp | missense_variant | 8/8 | 1 | NM_001256447.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000898 AC: 1AN: 111369Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33581
GnomAD3 exomes AF: 0.00000574 AC: 1AN: 174163Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 60041
GnomAD4 exome AF: 0.00000914 AC: 10AN: 1093648Hom.: 0 Cov.: 30 AF XY: 0.00000834 AC XY: 3AN XY: 359838
GnomAD4 genome ? AF: 0.00000898 AC: 1AN: 111369Hom.: 0 Cov.: 23 AF XY: 0.0000298 AC XY: 1AN XY: 33581
ClinVar
Submissions by phenotype
Severe motor and intellectual disabilities-sensorineural deafness-dystonia syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory of genome editing, Research Centre for Medical Genetics | Sep 22, 2023 | PM2, PP1, PP3 - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Oct 04, 2023 | This sequence change replaces glycine, which is neutral and non-polar, with aspartic acid, which is acidic and polar, at codon 239 of the BCAP31 protein (p.Gly239Asp). This variant is present in population databases (no rsID available, gnomAD 0.001%). This missense change has been observed in individual(s) with BCAP31-related conditions (PMID: 35887114). ClinVar contains an entry for this variant (Variation ID: 1347813). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. 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