11-59148707-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_001312911.2(FAM111A):c.-166C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00544 in 570,422 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0049 ( 1 hom., cov: 32)
Exomes 𝑓: 0.0056 ( 9 hom. )
Consequence
FAM111A
NM_001312911.2 5_prime_UTR
NM_001312911.2 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.150
Genes affected
FAM111A (HGNC:24725): (FAM111 trypsin like peptidase A) The protein encoded by this gene is cell-cycle regulated, and has nuclear localization. The C-terminal half of the protein shares homology with trypsin-like peptidases and it contains a PCNA-interacting peptide (PIP) box, that is necessary for its co-localization with proliferating cell nuclear antigen (PCNA). Reduced expression of this gene resulted in DNA replication defects, consistent with the demonstrated role for this gene in Simian Virus 40 (SV40) viral replication. Mutations in this gene have been associated with Kenny-Caffey syndrome (KCS) type 2 and the more severe osteocraniostenosis (OCS, also known as Gracile Bone Dysplasia), both characterized by short stature, hypoparathyroidism, bone development abnormalities, and hypocalcemia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -16 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 11-59148707-C-T is Benign according to our data. Variant chr11-59148707-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1197694.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High AC in GnomAd4 at 750 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FAM111A | NM_001312909.2 | c.-76-90C>T | intron_variant | Intron 4 of 5 | ENST00000675163.1 | NP_001299838.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00493 AC: 750AN: 152158Hom.: 1 Cov.: 32
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GnomAD4 exome AF: 0.00562 AC: 2351AN: 418146Hom.: 9 Cov.: 3 AF XY: 0.00550 AC XY: 1209AN XY: 219840
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GnomAD4 genome AF: 0.00493 AC: 750AN: 152276Hom.: 1 Cov.: 32 AF XY: 0.00540 AC XY: 402AN XY: 74456
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ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: not provided
- -
Sep 08, 2020
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
- -
Computational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at