rs17150692
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Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_017946.4(FKBP14):c.165C>T(p.Tyr55=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0186 in 1,612,990 control chromosomes in the GnomAD database, including 404 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.019 ( 47 hom., cov: 33)
Exomes 𝑓: 0.018 ( 357 hom. )
Consequence
FKBP14
NM_017946.4 synonymous
NM_017946.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.81
Genes affected
FKBP14 (HGNC:18625): (FKBP prolyl isomerase 14) The protein encoded by this gene is a member of the FK506-binding protein family of peptidyl-prolyl cis-trans isomerases. The encoded protein is found in the lumen of the endoplasmic reticulum, where it is thought to accelerate protein folding. Defects in this gene are a cause of a type of Ehlers-Danlos syndrome (EDS). Both a protein-coding variant and noncoding variants are transcribed from this gene. [provided by RefSeq, Mar 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.54).
BP6
?
Variant 7-30026344-G-A is Benign according to our data. Variant chr7-30026344-G-A is described in ClinVar as [Benign]. Clinvar id is 384694.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-30026344-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=1.81 with no splicing effect.
BA1
?
GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0578 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FKBP14 | NM_017946.4 | c.165C>T | p.Tyr55= | synonymous_variant | 1/4 | ENST00000222803.10 | |
FKBP14 | XM_047420550.1 | c.165C>T | p.Tyr55= | synonymous_variant | 1/4 | ||
FKBP14 | NR_046478.2 | n.359C>T | non_coding_transcript_exon_variant | 1/5 | |||
FKBP14 | NR_046479.2 | n.359C>T | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FKBP14 | ENST00000222803.10 | c.165C>T | p.Tyr55= | synonymous_variant | 1/4 | 1 | NM_017946.4 | P1 | |
FKBP14-AS1 | ENST00000422239.6 | n.1637G>A | non_coding_transcript_exon_variant | 4/4 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0194 AC: 2954AN: 152182Hom.: 46 Cov.: 33
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GnomAD3 exomes AF: 0.0245 AC: 6149AN: 250820Hom.: 134 AF XY: 0.0229 AC XY: 3111AN XY: 135616
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GnomAD4 exome AF: 0.0185 AC: 27013AN: 1460690Hom.: 357 Cov.: 31 AF XY: 0.0183 AC XY: 13273AN XY: 726726
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GnomAD4 genome ? AF: 0.0194 AC: 2955AN: 152300Hom.: 47 Cov.: 33 AF XY: 0.0191 AC XY: 1425AN XY: 74458
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ClinVar
Significance: Benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 07, 2016 | - - |
Ehlers-Danlos syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jul 16, 2022 | - - |
Ehlers-Danlos syndrome, kyphoscoliotic type, 2 Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 04, 2018 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
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Name
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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