rs796065022
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_StrongPP5
The NM_198488.5(FAM83H):c.1872_1873del(p.Leu625AlafsTer79) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 34)
Consequence
FAM83H
NM_198488.5 frameshift
NM_198488.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.42
Genes affected
FAM83H (HGNC:24797): (family with sequence similarity 83 member H) The protein encoded by this gene plays an important role in the structural development and calcification of tooth enamel. Defects in this gene are a cause of amelogenesis imperfecta type 3 (AI3). [provided by RefSeq, Mar 2010]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 5 ACMG points.
PVS1
?
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 4 pathogenic variants in the truncated region.
PP5
?
Variant 8-143727587-AGG-A is Pathogenic according to our data. Variant chr8-143727587-AGG-A is described in ClinVar as [Pathogenic]. Clinvar id is 779.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM83H | NM_198488.5 | c.1872_1873del | p.Leu625AlafsTer79 | frameshift_variant | 5/5 | ENST00000388913.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM83H | ENST00000388913.4 | c.1872_1873del | p.Leu625AlafsTer79 | frameshift_variant | 5/5 | 5 | NM_198488.5 | P2 | |
FAM83H | ENST00000650760.1 | c.2475_2476del | p.Leu826AlafsTer79 | frameshift_variant | 5/5 | A2 | |||
FAM83H | ENST00000395103.2 | c.1052_1053del | p.Leu352AlafsTer79 | frameshift_variant, NMD_transcript_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD3 genomes
?
Cov.:
34
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 34
GnomAD4 genome
?
Cov.:
34
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Amelogenesis imperfecta, hypocalcification type Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2009 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at