rs111450526
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_001256447.2(BCAP31):c.383C>T(p.Thr128Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00182 in 1,209,172 control chromosomes in the GnomAD database, including 1 homozygotes. There are 697 hemizygotes in GnomAD. In-silico tool predicts 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 -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCAP31 | NM_001256447.2 | c.383C>T | p.Thr128Met | missense_variant | Exon 5 of 8 | ENST00000345046.12 | NP_001243376.1 | |
BCAP31 | NM_001139457.2 | c.584C>T | p.Thr195Met | missense_variant | Exon 5 of 8 | NP_001132929.1 | ||
BCAP31 | NM_001139441.1 | c.383C>T | p.Thr128Met | missense_variant | Exon 5 of 8 | NP_001132913.1 | ||
BCAP31 | NM_005745.8 | c.383C>T | p.Thr128Met | missense_variant | Exon 5 of 8 | NP_005736.3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00137 AC: 154AN: 112483Hom.: 0 Cov.: 24 AF XY: 0.00144 AC XY: 50AN XY: 34641
GnomAD3 exomes AF: 0.00138 AC: 253AN: 183054Hom.: 0 AF XY: 0.00136 AC XY: 92AN XY: 67502
GnomAD4 exome AF: 0.00187 AC: 2046AN: 1096636Hom.: 1 Cov.: 30 AF XY: 0.00179 AC XY: 647AN XY: 362056
GnomAD4 genome AF: 0.00137 AC: 154AN: 112536Hom.: 0 Cov.: 24 AF XY: 0.00144 AC XY: 50AN XY: 34704
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:5
Likely benign, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | May 10, 2016 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2017 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 14, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 20, 2025 | - - |
BCAP31-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 23, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at