chr17-41813025-TCCAGGCACCATGTTCCCCGCGGGCCCCCCCAGCCACAGCCTCCTCCGGCTCCCCCTGCTGCAGTTGCTGCTACTGGTGGTGCAGGC-T
Variant summary
Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1PP5_Moderate
The NM_021939.4(FKBP10):c.-8_78delCAGGCACCATGTTCCCCGCGGGCCCCCCCAGCCACAGCCTCCTCCGGCTCCCCCTGCTGCAGTTGCTGCTACTGGTGGTGCAGGCC(p.Met1fs) variant causes a frameshift, start lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Consequence
NM_021939.4 frameshift, start_lost
Scores
Clinical Significance
Conservation
Publications
- Bruck syndrome 1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- osteogenesis imperfecta type 11Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, Illumina
- osteogenesis imperfecta type 3Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- osteogenesis imperfecta type 4Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- arthrogryposis-like syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- Bruck syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Pathogenic. The variant received 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FKBP10 | NM_021939.4 | c.-8_78delCAGGCACCATGTTCCCCGCGGGCCCCCCCAGCCACAGCCTCCTCCGGCTCCCCCTGCTGCAGTTGCTGCTACTGGTGGTGCAGGCC | p.Met1fs | frameshift_variant, start_lost | Exon 1 of 10 | ENST00000321562.9 | NP_068758.3 | |
FKBP10 | NM_021939.4 | c.-8_78delCAGGCACCATGTTCCCCGCGGGCCCCCCCAGCCACAGCCTCCTCCGGCTCCCCCTGCTGCAGTTGCTGCTACTGGTGGTGCAGGCC | 5_prime_UTR_variant | Exon 1 of 10 | ENST00000321562.9 | NP_068758.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FKBP10 | ENST00000321562.9 | c.-8_78delCAGGCACCATGTTCCCCGCGGGCCCCCCCAGCCACAGCCTCCTCCGGCTCCCCCTGCTGCAGTTGCTGCTACTGGTGGTGCAGGCC | p.Met1fs | frameshift_variant, start_lost | Exon 1 of 10 | 1 | NM_021939.4 | ENSP00000317232.4 | ||
FKBP10 | ENST00000321562.9 | c.-8_78delCAGGCACCATGTTCCCCGCGGGCCCCCCCAGCCACAGCCTCCTCCGGCTCCCCCTGCTGCAGTTGCTGCTACTGGTGGTGCAGGCC | 5_prime_UTR_variant | Exon 1 of 10 | 1 | NM_021939.4 | ENSP00000317232.4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at