rs1553663498
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_015175.3(NBEAL2):c.4081G>T(p.Glu1361Ter) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000109 in 1,461,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.000011 ( 0 hom. )
Consequence
NBEAL2
NM_015175.3 stop_gained
NM_015175.3 stop_gained
Scores
4
2
1
Clinical Significance
Conservation
PhyloP100: 4.99
Genes affected
NBEAL2 (HGNC:31928): (neurobeachin like 2) The protein encoded by this gene contains a beige and Chediak-Higashi (BEACH) domain and multiple WD40 domains, and may play a role in megakaryocyte alpha-granule biogenesis. Mutations in this gene are a cause of gray platelet syndrome. [provided by RefSeq, Dec 2011]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 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 3-47000180-G-T is Pathogenic according to our data. Variant chr3-47000180-G-T is described in ClinVar as [Pathogenic]. Clinvar id is 435928.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NBEAL2 | NM_015175.3 | c.4081G>T | p.Glu1361Ter | stop_gained | 27/54 | ENST00000450053.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NBEAL2 | ENST00000450053.8 | c.4081G>T | p.Glu1361Ter | stop_gained | 27/54 | 2 | NM_015175.3 | P2 | |
NBEAL2 | ENST00000416683.5 | c.1960-16G>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | |||||
NBEAL2 | ENST00000651747.1 | c.3979G>T | p.Glu1327Ter | stop_gained | 26/53 | A2 | |||
NBEAL2 | ENST00000652744.1 | n.418G>T | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461554Hom.: 0 Cov.: 33 AF XY: 0.0000110 AC XY: 8AN XY: 727070
GnomAD4 exome
AF:
AC:
16
AN:
1461554
Hom.:
Cov.:
33
AF XY:
AC XY:
8
AN XY:
727070
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
NBEAL2-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Sep 29, 2023 | The NBEAL2 c.4081G>T variant is predicted to result in premature protein termination (p.Glu1361*). This variant has been reported in the compound heterozygous state in an individual with Grey platelet syndrome (Sims et al. 2020. PubMed ID: 32693407. Supplement file 2). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Nonsense variants in NBEAL2 are expected to be pathogenic. This variant is interpreted as pathogenic. - |
Gray platelet syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Dec 28, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
MutationTaster
Benign
A;D;D
Vest4
GERP RS
Splicing
Name
Calibrated prediction
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Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 16
Find out detailed SpliceAI scores and Pangolin per-transcript scores at