7-73330268-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_003602.5(FKBP6):c.384C>T(p.Pro128Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000278 in 1,614,150 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00042 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00026 ( 1 hom. )
Consequence
FKBP6
NM_003602.5 synonymous
NM_003602.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.03
Genes affected
FKBP6 (HGNC:3722): (FKBP prolyl isomerase family member 6 (inactive)) The protein encoded by this gene is a cis-trans peptidyl-prolyl isomerase that may function in immunoregulation and basic cellular processes involving protein folding and trafficking. This gene is located in a chromosomal region that is deleted in Williams-Beuren syndrome. Defects in this gene may cause male infertility. There are multiple pseudogenes for this gene located nearby on chromosome 7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.58).
BP6
Variant 7-73330268-C-T is Benign according to our data. Variant chr7-73330268-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2657550.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.03 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FKBP6 | NM_003602.5 | c.384C>T | p.Pro128Pro | synonymous_variant | 4/9 | ENST00000252037.5 | NP_003593.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FKBP6 | ENST00000252037.5 | c.384C>T | p.Pro128Pro | synonymous_variant | 4/9 | 1 | NM_003602.5 | ENSP00000252037.4 |
Frequencies
GnomAD3 genomes AF: 0.000421 AC: 64AN: 152190Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000310 AC: 78AN: 251492Hom.: 0 AF XY: 0.000375 AC XY: 51AN XY: 135922
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GnomAD4 exome AF: 0.000263 AC: 384AN: 1461842Hom.: 1 Cov.: 32 AF XY: 0.000283 AC XY: 206AN XY: 727224
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GnomAD4 genome AF: 0.000420 AC: 64AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000443 AC XY: 33AN XY: 74496
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2022 | FKBP6: BP4, BP7 - |
Computational scores
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Benign
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Benign
DANN
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at