chr6-111714405-G-A
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3PP5
The NM_002037.5(FYN):c.286C>T(p.Arg96Trp) variant causes a missense 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 Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
FYN
NM_002037.5 missense
NM_002037.5 missense
Scores
8
8
3
Clinical Significance
Conservation
PhyloP100: 1.36
Genes affected
FYN (HGNC:4037): (FYN proto-oncogene, Src family tyrosine kinase) This gene is a member of the protein-tyrosine kinase oncogene family. It encodes a membrane-associated tyrosine kinase that has been implicated in the control of cell growth. The protein associates with the p85 subunit of phosphatidylinositol 3-kinase and interacts with the fyn-binding protein. Alternatively spliced transcript variants encoding distinct isoforms exist. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.816
PP5
Variant 6-111714405-G-A is Pathogenic according to our data. Variant chr6-111714405-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 2681289.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FYN | NM_002037.5 | c.286C>T | p.Arg96Trp | missense_variant | 5/14 | ENST00000354650.7 | NP_002028.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FYN | ENST00000354650.7 | c.286C>T | p.Arg96Trp | missense_variant | 5/14 | 1 | NM_002037.5 | ENSP00000346671 | P3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
EBV-positive nodal T- and NK-cell lymphoma Pathogenic:1
Pathogenic, no assertion criteria provided | research | Department of Clinical Pathology, School of Medicine, Fujita Health University | - | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
.;.;D;.;D;.;T;T;.;T;T;T;T;T;.;T;D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
D;.;.;D;D;.;D;D;D;D;D;D;D;D;D;D;D
M_CAP
Benign
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Pathogenic
M;M;M;M;M;M;.;.;.;.;.;.;.;.;.;.;.
MutationTaster
Benign
A;D;D;D;D;D;D;D;D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
REVEL
Uncertain
Sift
Benign
T;T;T;T;T;T;T;D;D;D;D;D;D;D;D;D;D
Sift4G
Uncertain
D;D;D;D;D;D;.;.;.;T;.;D;.;T;D;.;D
Polyphen
1.0, 0.83
.;.;D;P;D;.;.;.;.;.;.;.;.;.;.;.;.
Vest4
MutPred
Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);Gain of catalytic residue at R96 (P = 0.0233);
MVP
MPC
2.4
ClinPred
D
GERP RS
Varity_R
gMVP
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
No publications associated with this variant yet.