chr6-111719926-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_002037.5(FYN):c.126C>T(p.Phe42=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00201 in 1,614,160 control chromosomes in the GnomAD database, including 52 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.011 ( 27 hom., cov: 32)
Exomes 𝑓: 0.0010 ( 25 hom. )
Consequence
FYN
NM_002037.5 synonymous
NM_002037.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.680
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 Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.42).
BP6
?
Variant 6-111719926-G-A is Benign according to our data. Variant chr6-111719926-G-A is described in ClinVar as [Benign]. Clinvar id is 709055.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.68 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0114 (1735/152270) while in subpopulation AFR AF= 0.0396 (1644/41534). AF 95% confidence interval is 0.038. There are 27 homozygotes in gnomad4. There are 833 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1736 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FYN | NM_002037.5 | c.126C>T | p.Phe42= | synonymous_variant | 4/14 | ENST00000354650.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FYN | ENST00000354650.7 | c.126C>T | p.Phe42= | synonymous_variant | 4/14 | 1 | NM_002037.5 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.0114 AC: 1736AN: 152152Hom.: 27 Cov.: 32
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GnomAD3 exomes AF: 0.00285 AC: 717AN: 251390Hom.: 17 AF XY: 0.00209 AC XY: 284AN XY: 135872
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GnomAD4 exome AF: 0.00103 AC: 1510AN: 1461890Hom.: 25 Cov.: 30 AF XY: 0.000875 AC XY: 636AN XY: 727246
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 16, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at