rs1060505056
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_001465.6(FYB1):c.1385_1386delAT(p.Tyr462fs) variant causes a frameshift change. The variant allele was found at a frequency of 0.000000731 in 1,367,934 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 7.3e-7 ( 0 hom. )
Consequence
FYB1
NM_001465.6 frameshift
NM_001465.6 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 4.98
Publications
1 publications found
Genes affected
FYB1 (HGNC:4036): (FYN binding protein 1) The protein encoded by this gene is an adapter for the FYN protein and LCP2 signaling cascades in T-cells. The encoded protein is involved in platelet activation and controls the expression of interleukin-2. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2011]
FYB1 Gene-Disease associations (from GenCC):
- thrombocytopenia 3Inheritance: AR Classification: STRONG, MODERATE Submitted by: ClinGen, 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 5-39138664-CAT-C is Pathogenic according to our data. Variant chr5-39138664-CAT-C is described in ClinVar as Pathogenic. ClinVar VariationId is 417970.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FYB1 | NM_001465.6 | c.1385_1386delAT | p.Tyr462fs | frameshift_variant | Exon 6 of 19 | ENST00000512982.4 | NP_001456.3 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| FYB1 | ENST00000512982.4 | c.1385_1386delAT | p.Tyr462fs | frameshift_variant | Exon 6 of 19 | 2 | NM_001465.6 | ENSP00000425845.3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 7.31e-7 AC: 1AN: 1367934Hom.: 0 AF XY: 0.00000146 AC XY: 1AN XY: 684042 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
1367934
Hom.:
AF XY:
AC XY:
1
AN XY:
684042
show subpopulations
African (AFR)
AF:
AC:
0
AN:
31160
American (AMR)
AF:
AC:
0
AN:
41438
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
25080
East Asian (EAS)
AF:
AC:
1
AN:
38932
South Asian (SAS)
AF:
AC:
0
AN:
80852
European-Finnish (FIN)
AF:
AC:
0
AN:
52792
Middle Eastern (MID)
AF:
AC:
0
AN:
5490
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1035124
Other (OTH)
AF:
AC:
0
AN:
57066
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
8
10
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Thrombocytopenia 3 Pathogenic:1
Dec 23, 2020
OMIM
Significance:Pathogenic
Review Status:no assertion criteria provided
Collection Method:literature only
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
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
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