chr5-108867763-T-TC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_005246.4(FER):c.482-3dup variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00208 in 1,589,370 control chromosomes in the GnomAD database, including 33 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.012 ( 31 hom., cov: 30)
Exomes 𝑓: 0.0010 ( 2 hom. )
Consequence
FER
NM_005246.4 splice_region, splice_polypyrimidine_tract, intron
NM_005246.4 splice_region, splice_polypyrimidine_tract, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: -0.268
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 -10 ACMG points.
BP6
?
Variant 5-108867763-T-TC is Benign according to our data. Variant chr5-108867763-T-TC is described in ClinVar as [Benign]. Clinvar id is 719488.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0122 (1839/150586) while in subpopulation AFR AF= 0.0426 (1731/40680). AF 95% confidence interval is 0.0409. There are 31 homozygotes in gnomad4. There are 844 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
BS2
?
High AC in GnomAd at 1835 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FER | NM_005246.4 | c.482-3dup | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000281092.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FER | ENST00000281092.9 | c.482-3dup | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_005246.4 | P1 | |||
FER | ENST00000504143.6 | c.208-3dup | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0122 AC: 1835AN: 150478Hom.: 31 Cov.: 30
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GnomAD3 exomes AF: 0.00276 AC: 626AN: 227112Hom.: 6 AF XY: 0.00179 AC XY: 220AN XY: 123024
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GnomAD4 exome AF: 0.00101 AC: 1460AN: 1438784Hom.: 2 Cov.: 34 AF XY: 0.000865 AC XY: 619AN XY: 715374
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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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at