chr5-108959248-T-C
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BS1BS2
The NM_005246.4(FER):c.1557T>C(p.Thr519=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00181 in 1,611,680 control chromosomes in the GnomAD database, including 42 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.010 ( 22 hom., cov: 32)
Exomes 𝑓: 0.00094 ( 20 hom. )
Consequence
FER
NM_005246.4 synonymous
NM_005246.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.25
Genes affected
FER (HGNC:3655): (FER tyrosine kinase) The protein encoded by this gene is a member of the FPS/FES family of non-transmembrane receptor tyrosine kinases. It regulates cell-cell adhesion and mediates signaling from the cell surface to the cytoskeleton via growth factor receptors. Alternative splicing results in multiple transcript variants. A related pseudogene has been identified on chromosome X. [provided by RefSeq, Apr 2015]
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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=-0.46).
BP6
?
Variant 5-108959248-T-C is Benign according to our data. Variant chr5-108959248-T-C is described in ClinVar as [Benign]. Clinvar id is 792007.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.25 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0102 (1544/151972) while in subpopulation AFR AF= 0.0355 (1473/41536). AF 95% confidence interval is 0.034. There are 22 homozygotes in gnomad4. There are 728 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1541 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FER | NM_005246.4 | c.1557T>C | p.Thr519= | synonymous_variant | 13/20 | ENST00000281092.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FER | ENST00000281092.9 | c.1557T>C | p.Thr519= | synonymous_variant | 13/20 | 1 | NM_005246.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0101 AC: 1541AN: 151854Hom.: 22 Cov.: 32
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GnomAD3 exomes AF: 0.00257 AC: 643AN: 250200Hom.: 16 AF XY: 0.00183 AC XY: 247AN XY: 135298
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GnomAD4 exome AF: 0.000945 AC: 1379AN: 1459708Hom.: 20 Cov.: 30 AF XY: 0.000793 AC XY: 576AN XY: 726156
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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 | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at