chrX-153700965-T-A
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001256447.2(BCAP31):c.713A>T(p.Asp238Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000232 in 1,205,078 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. D238D) has been classified as Likely benign.
Frequency
Consequence
NM_001256447.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BCAP31 | NM_001256447.2 | c.713A>T | p.Asp238Val | missense_variant | 8/8 | ENST00000345046.12 | |
BCAP31 | NM_001139457.2 | c.914A>T | p.Asp305Val | missense_variant | 8/8 | ||
BCAP31 | NM_001139441.1 | c.713A>T | p.Asp238Val | missense_variant | 8/8 | ||
BCAP31 | NM_005745.8 | c.713A>T | p.Asp238Val | missense_variant | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BCAP31 | ENST00000345046.12 | c.713A>T | p.Asp238Val | missense_variant | 8/8 | 1 | NM_001256447.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000898 AC: 1AN: 111401Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33593
GnomAD3 exomes AF: 0.0000402 AC: 7AN: 174088Hom.: 0 AF XY: 0.0000667 AC XY: 4AN XY: 59992
GnomAD4 exome AF: 0.0000247 AC: 27AN: 1093677Hom.: 0 Cov.: 29 AF XY: 0.0000306 AC XY: 11AN XY: 359871
GnomAD4 genome ? AF: 0.00000898 AC: 1AN: 111401Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33593
ClinVar
Submissions by phenotype
Microcephaly Uncertain:1
Uncertain significance, no assertion criteria provided | research | Department of Pediatrics, Samsung Medical Center, Samsung Medical Center | - | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 15, 2022 | 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 813609). This variant has not been reported in the literature in individuals affected with BCAP31-related conditions. This variant is present in population databases (rs782155363, gnomAD 0.05%). This sequence change replaces aspartic acid, which is acidic and polar, with valine, which is neutral and non-polar, at codon 238 of the BCAP31 protein (p.Asp238Val). - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2023 | 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