rs6916861
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_002037.5(FYN):c.*685T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,026 control chromosomes in the GnomAD database, including 3,631 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.19 ( 3631 hom., cov: 32)
Exomes 𝑓: 0.13 ( 0 hom. )
Consequence
FYN
NM_002037.5 3_prime_UTR
NM_002037.5 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.610
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 -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FYN | NM_002037.5 | c.*685T>G | 3_prime_UTR_variant | 14/14 | ENST00000354650.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FYN | ENST00000354650.7 | c.*685T>G | 3_prime_UTR_variant | 14/14 | 1 | NM_002037.5 | P3 | ||
FYN | ENST00000368682.8 | c.*685T>G | 3_prime_UTR_variant | 14/14 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.192 AC: 29240AN: 151900Hom.: 3625 Cov.: 32
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GnomAD4 exome AF: 0.125 AC: 1AN: 8Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 6
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GnomAD4 genome ? AF: 0.193 AC: 29265AN: 152018Hom.: 3631 Cov.: 32 AF XY: 0.191 AC XY: 14168AN XY: 74318
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at