Variant chr6-111714402-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5

The NM_002037.5(FYN):c.289A>G(p.Thr97Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

FYN
NM_002037.5 missense

Scores

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 8.02

Variant links:

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]

FYN links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP5

Variant 6-111714402-T-C is Pathogenic according to our data. Variant chr6-111714402-T-C is described in ClinVar as [Pathogenic]. Clinvar id is 2681290.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 linkuse as main transcript	c.289A>G	p.Thr97Ala	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 linkuse as main transcript	c.289A>G	p.Thr97Ala	missense_variant	5/14	1	NM_002037.5	ENSP00000346671	P3	P06241-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

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: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.65

BayesDel_addAF

Uncertain

0.079

BayesDel_noAF

Benign

-0.12

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Uncertain

0.46

.;.;T;.;T;.;T;T;.;T;T;T;T;T;.;T;T

Eigen

Benign

-0.095

Eigen_PC

Benign

0.14

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.83

T;.;.;T;T;.;T;T;T;T;T;T;T;D;D;D;D

M_CAP

Benign

0.020

MetaRNN

Uncertain

0.44

T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.0

L;L;L;L;L;L;.;.;.;.;.;.;.;.;.;.;.

MutationTaster

Benign

1.0

D;D;D;D;D;D;D;D;D

PrimateAI

Pathogenic

0.88

PROVEAN

Uncertain

-2.5

D;D;N;N;N;D;D;D;D;D;D;D;D;D;D;D;D

REVEL

Benign

0.23

Sift

Benign

0.095

T;T;T;T;T;T;D;D;D;D;D;D;D;D;D;D;D

Sift4G

Benign

0.55

T;T;T;T;T;T;.;.;.;D;.;D;.;D;D;.;D

Polyphen

0.0060, 0.0090

.;.;B;B;B;.;.;.;.;.;.;.;.;.;.;.;.

Vest4

0.64

MutPred

0.44

Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);Loss of phosphorylation at T97 (P = 0.033);

MVP

0.86

MPC

1.1

ClinPred

0.81

GERP RS

5.8

Varity_R

0.43

gMVP

0.58

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over