chr13-101721607-C-CTAAT
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Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_004115.4(FGF14):c.*1220_*1223dupATTA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000611 in 152,126 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00061 ( 0 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
FGF14
NM_004115.4 3_prime_UTR
NM_004115.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.51
Genes affected
FGF14 (HGNC:3671): (fibroblast growth factor 14) The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members possess broad mitogenic and cell survival activities, and are involved in a variety of biological processes, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth and invasion. A mutation in this gene is associated with autosomal dominant cerebral ataxia. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP6
Variant 13-101721607-C-CTAAT is Benign according to our data. Variant chr13-101721607-C-CTAAT is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 310869.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Benign=1}.
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000611 (93/152126) while in subpopulation NFE AF= 0.00112 (76/67986). AF 95% confidence interval is 0.000915. There are 0 homozygotes in gnomad4. There are 40 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 93 AD gene.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| FGF14 | NM_004115.4 | c.*1220_*1223dupATTA | 3_prime_UTR_variant | 5/5 | ENST00000376143.5 | NP_004106.1 |
Ensembl
Frequencies
GnomAD3 genomes 0.000612 AC: 93AN: 152008Hom.: 0 Cov.: 32
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome 0.000611 AC: 93AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.000538 AC XY: 40AN XY: 74368
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Autosomal dominant cerebellar ataxia Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
| Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2022 | FGF14: BS1, BS2 - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at