chrX-153702090-T-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001256447.2(BCAP31):c.619A>G(p.Asn207Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000307 in 1,204,837 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 19 hemizygotes in GnomAD. 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001256447.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCAP31 | NM_001256447.2 | c.619A>G | p.Asn207Asp | missense_variant | 7/8 | ENST00000345046.12 | |
BCAP31 | NM_001139457.2 | c.820A>G | p.Asn274Asp | missense_variant | 7/8 | ||
BCAP31 | NM_001139441.1 | c.619A>G | p.Asn207Asp | missense_variant | 7/8 | ||
BCAP31 | NM_005745.8 | c.619A>G | p.Asn207Asp | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAP31 | ENST00000345046.12 | c.619A>G | p.Asn207Asp | missense_variant | 7/8 | 1 | NM_001256447.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000532 AC: 6AN: 112794Hom.: 0 Cov.: 24 AF XY: 0.0000572 AC XY: 2AN XY: 34942
GnomAD3 exomes AF: 0.0000334 AC: 6AN: 179749Hom.: 0 AF XY: 0.0000466 AC XY: 3AN XY: 64441
GnomAD4 exome AF: 0.0000284 AC: 31AN: 1092043Hom.: 0 Cov.: 28 AF XY: 0.0000475 AC XY: 17AN XY: 357625
GnomAD4 genome ? AF: 0.0000532 AC: 6AN: 112794Hom.: 0 Cov.: 24 AF XY: 0.0000572 AC XY: 2AN XY: 34942
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 20, 2023 | This sequence change replaces asparagine, which is neutral and polar, with aspartic acid, which is acidic and polar, at codon 207 of the BCAP31 protein (p.Asn207Asp). This variant is present in population databases (rs201920029, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with BCAP31-related conditions. 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. - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 22, 2022 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at