rs761069193
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_017679.5(BCAS3):c.576C>A(p.Cys192*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
BCAS3
NM_017679.5 stop_gained
NM_017679.5 stop_gained
Scores
2
4
1
Clinical Significance
Conservation
PhyloP100: 2.96
Publications
1 publications found
Genes affected
BCAS3 (HGNC:14347): (BCAS3 microtubule associated cell migration factor) Enables several functions, including acetyltransferase activator activity; beta-tubulin binding activity; and histone acetyltransferase binding activity. Involved in cellular response to estrogen stimulus; positive regulation of catalytic activity; and positive regulation of transcription by RNA polymerase II. Located in nucleus; phagophore assembly site; and transcriptionally active chromatin. Biomarker of breast cancer. [provided by Alliance of Genome Resources, Apr 2022]
BCAS3 Gene-Disease associations (from GenCC):
- Hengel-Maroofian-Schols syndromeInheritance: AR Classification: STRONG Submitted by: G2P, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 11 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-60868675-C-A is Pathogenic according to our data. Variant chr17-60868675-C-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1048568.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1420590Hom.: 0 Cov.: 26 AF XY: 0.00 AC XY: 0AN XY: 707056
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1420590
Hom.:
Cov.:
26
AF XY:
AC XY:
0
AN XY:
707056
African (AFR)
AF:
AC:
0
AN:
30826
American (AMR)
AF:
AC:
0
AN:
37630
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25130
East Asian (EAS)
AF:
AC:
0
AN:
37764
South Asian (SAS)
AF:
AC:
0
AN:
80402
European-Finnish (FIN)
AF:
AC:
0
AN:
53018
Middle Eastern (MID)
AF:
AC:
0
AN:
5636
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1091402
Other (OTH)
AF:
AC:
0
AN:
58782
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Global developmental delay Pathogenic:1
Jan 12, 2021
Section for Clinical Neurogenetics, University of Tübingen
Significance:Likely pathogenic
Review Status:no assertion criteria provided
Collection Method:research
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
DANN
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
PhyloP100
Vest4
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.