rs796051853
Variant summary
Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PVS1PM2PP3_StrongPP5
The NM_020223.4(FAM20C):c.1364-2A>G variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000578 in 1,384,746 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_020223.4 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FAM20C | NM_020223.4 | c.1364-2A>G | splice_acceptor_variant | ENST00000313766.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FAM20C | ENST00000313766.6 | c.1364-2A>G | splice_acceptor_variant | 1 | NM_020223.4 | P1 | |||
FAM20C | ENST00000515795.1 | n.1021-2A>G | splice_acceptor_variant, non_coding_transcript_variant | 1 | |||||
FAM20C | ENST00000512382.1 | n.570-2A>G | splice_acceptor_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 34
GnomAD4 exome AF: 0.00000578 AC: 8AN: 1384746Hom.: 0 Cov.: 31 AF XY: 0.00000732 AC XY: 5AN XY: 683308
GnomAD4 genome ? Cov.: 34
ClinVar
Submissions by phenotype
Lethal osteosclerotic bone dysplasia Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2007 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at