rs749027804
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_020198.3(CCDC47):c.811C>T(p.Arg271Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,461,314 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_020198.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCDC47 | NM_020198.3 | c.811C>T | p.Arg271Ter | stop_gained | 7/13 | ENST00000225726.10 | |
CCDC47 | XM_005257527.3 | c.811C>T | p.Arg271Ter | stop_gained | 7/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCDC47 | ENST00000225726.10 | c.811C>T | p.Arg271Ter | stop_gained | 7/13 | 1 | NM_020198.3 | P1 | |
CCDC47 | ENST00000403162.7 | c.811C>T | p.Arg271Ter | stop_gained | 8/14 | 2 | P1 | ||
CCDC47 | ENST00000582252.1 | c.811C>T | p.Arg271Ter | stop_gained | 7/12 | 2 | |||
CCDC47 | ENST00000582331.2 | n.450C>T | non_coding_transcript_exon_variant | 3/6 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251424Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135880
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461314Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726972
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Trichohepatoneurodevelopmental syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 02, 2019 | - - |
Global developmental delay with dysmorphic features, liver dysfunction, pruritus, and woolly hair Pathogenic:1
Likely pathogenic, criteria provided, single submitter | research | Undiagnosed Diseases Program Translational Research Laboratory, National Institutes of Health | Sep 24, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at